{ "conflicts": [], "coverage": { "cells": { "RBP-closed": { "af_prediction": 0, "md": 0, "saxs_sans": 0, "xray": 5 }, "RBP-open": { "af_prediction": 0, "md": 0, "saxs_sans": 0, "xray": 1 } }, "data_levels": { "RBP-closed": { "xray": "processed" }, "RBP-open": { "xray": "processed" } }, "single_method_states": [ "RBP-open", "RBP-closed" ], "states": [ "RBP-open", "RBP-closed" ], "techniques": [ "xray", "saxs_sans", "af_prediction", "md" ], "unmapped_evidence": 12 }, "curation": { "as_of": "2026-10-19", "curator": "draft (unreviewed)", "file": "P02925.yaml", "status": "draft" }, "evidence": [ { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 7.0, "salt_mM": null, "temperature_c": -183.15 }, "construct": { "description": "D-RIBOSE-BINDING PROTEIN (chains A,B)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/1BA2", "evidence_id": "EV-PDB-1BA2-1", "mappings": [], "molecule_id": "P02925", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.1 }, "provenance": { "deposit_id": "1BA2", "doi": "10.1006/jmbi.1998.1785", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/1BA2" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "D67R MUTANT OF D-RIBOSE-BINDING PROTEIN FROM ESCHERICHIA COLI" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "RIP" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "D-RIBOSE-BINDING PROTEIN (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/1DBP", "evidence_id": "EV-PDB-1DBP-1", "mappings": [ { "confidence": "high", "justification": "Ribose (RIP) bound closes the two domains.", "rule": "rbp-ribose-closed", "state_id": "RBP-closed", "who": "rule:rbp-ribose-closed" } ], "molecule_id": "P02925", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.2 }, "provenance": { "deposit_id": "1DBP", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/1DBP" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "IDENTICAL MUTATIONS AT CORRESPONDING POSITIONS IN TWO HOMOLOGOUS PROTEINS WITH NON-IDENTICAL EFFECTS" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "RIP" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "D-RIBOSE-BINDING PROTEIN (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/1DRJ", "evidence_id": "EV-PDB-1DRJ-1", "mappings": [ { "confidence": "high", "justification": "Ribose (RIP) bound closes the two domains.", "rule": "rbp-ribose-closed", "state_id": "RBP-closed", "who": "rule:rbp-ribose-closed" } ], "molecule_id": "P02925", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.5 }, "provenance": { "deposit_id": "1DRJ", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/1DRJ" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "PROBING PROTEIN-PROTEIN INTERACTIONS: THE RIBOSE-BINDING PROTEIN IN BACTERIAL TRANSPORT AND CHEMOTAXIS" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "RIP" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "D-RIBOSE-BINDING PROTEIN (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/1DRK", "evidence_id": "EV-PDB-1DRK-1", "mappings": [ { "confidence": "high", "justification": "Ribose (RIP) bound closes the two domains.", "rule": "rbp-ribose-closed", "state_id": "RBP-closed", "who": "rule:rbp-ribose-closed" } ], "molecule_id": "P02925", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.0 }, "provenance": { "deposit_id": "1DRK", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/1DRK" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "PROBING PROTEIN-PROTEIN INTERACTIONS: THE RIBOSE-BINDING PROTEIN IN BACTERIAL TRANSPORT AND CHEMOTAXIS" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 5.0, "salt_mM": null, "temperature_c": -183.15 }, "construct": { "description": "D-RIBOSE-BINDING PROTEIN (chains A,B,C,D)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/1URP", "evidence_id": "EV-PDB-1URP-1", "mappings": [ { "confidence": "high", "justification": "Ligand-free D-ribose-binding protein.", "rule": "curator_assignment", "state_id": "RBP-open", "who": "curator:draft (unreviewed)" } ], "molecule_id": "P02925", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 2.3 }, "provenance": { "deposit_id": "1URP", "doi": "10.1006/jmbi.1998.1785", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/1URP" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "D-RIBOSE-BINDING PROTEIN FROM ESCHERICHIA COLI" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "RIP" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "D-RIBOSE-BINDING PROTEIN (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2DRI", "evidence_id": "EV-PDB-2DRI-1", "mappings": [ { "confidence": "high", "justification": "Ribose (RIP) bound.", "rule": "curator_assignment", "state_id": "RBP-closed", "who": "curator:draft (unreviewed)" } ], "molecule_id": "P02925", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.6 }, "provenance": { "deposit_id": "2DRI", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2DRI" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "PROBING PROTEIN-PROTEIN INTERACTIONS: THE RIBOSE BINDING PROTEIN IN BACTERIAL TRANSPORT AND CHEMOTAXIS" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_vitro", "ions": [], "ligands": [ "RIP" ], "notes": "Entry-level ligand list; oligosaccharides appear as branched entities. pH and temperature are null when not deposited in machine-readable fields.", "ph": 5.0, "salt_mM": null, "temperature_c": -173.15 }, "construct": { "description": "D-ribose-binding periplasmic protein (chains A)", "labels": [] }, "data_format": "mmCIF + structure factors", "data_level": "processed", "data_link": "https://www.rcsb.org/structure/2GX6", "evidence_id": "EV-PDB-2GX6-1", "mappings": [ { "confidence": "high", "justification": "Ribose (RIP) bound closes the two domains.", "rule": "rbp-ribose-closed", "state_id": "RBP-closed", "who": "rule:rbp-ribose-closed" } ], "molecule_id": "P02925", "observable": { "type": "resolution", "uncertainty": null, "unit": "Å", "value": 1.97 }, "provenance": { "deposit_id": "2GX6", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://www.rcsb.org/structure/2GX6" }, "reader": null, "source_kind": "deposit", "technique": "xray", "title": "Rational stabilization of E. coli ribose binding protein" }, { "conditions": { "applied_force_pn": null, "buffer": "50 mM Tris, 50 mM NaCl, 10% glycerol", "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Other molecules in the sample are listed as partners; Rg is of the whole sample. Dmax 8.6 nm.", "ph": 7.0, "salt_mM": null, "temperature_c": 4.0 }, "construct": { "description": "Ribose import binding protein RbsB", "labels": [] }, "data_format": "scattering curve", "data_level": "processed", "data_link": "https://www.sasbdb.org/data/SASDSB9/", "evidence_id": "EV-SASBDB-SASDSB9", "mappings": [], "molecule_id": "P02925", "observable": { "type": "radius_of_gyration", "uncertainty": 0.002, "unit": "nm", "value": 2.086 }, "provenance": { "deposit_id": "SASDSB9", "doi": "10.1016/j.dib.2023.109932", "licence": "CC BY 4.0 (verify)", "retrieved": "2026-10-19", "source": "SASBDB", "url": "https://www.sasbdb.org/data/SASDSB9/" }, "reader": null, "source_kind": "deposit", "technique": "saxs_sans", "title": "SAXS/WAXS data of conformationally flexible ribose binding protein" }, { "conditions": { "applied_force_pn": null, "buffer": "50 mM Tris, 50 mM NaCl, 10% glycerol", "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Other molecules in the sample are listed as partners; Rg is of the whole sample. Dmax 8.4 nm.", "ph": 7.0, "salt_mM": null, "temperature_c": 4.0 }, "construct": { "description": "Ribose import binding protein RbsB", "labels": [] }, "data_format": "scattering curve", "data_level": "processed", "data_link": "https://www.sasbdb.org/data/SASDSC9/", "evidence_id": "EV-SASBDB-SASDSC9", "mappings": [], "molecule_id": "P02925", "observable": { "type": "radius_of_gyration", "uncertainty": 0.003, "unit": "nm", "value": 2.1 }, "provenance": { "deposit_id": "SASDSC9", "doi": "10.1016/j.dib.2023.109932", "licence": "CC BY 4.0 (verify)", "retrieved": "2026-10-19", "source": "SASBDB", "url": "https://www.sasbdb.org/data/SASDSC9/" }, "reader": null, "source_kind": "deposit", "technique": "saxs_sans", "title": "SAXS/WAXS data of conformationally flexible ribose binding protein" }, { "conditions": { "applied_force_pn": null, "buffer": "50 mM Tris, 50 mM NaCl, 10% glycerol", "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Other molecules in the sample are listed as partners; Rg is of the whole sample. Dmax 8.3 nm.", "ph": 7.0, "salt_mM": null, "temperature_c": 4.0 }, "construct": { "description": "Ribose import binding protein RbsB", "labels": [] }, "data_format": "scattering curve", "data_level": "processed", "data_link": "https://www.sasbdb.org/data/SASDSD9/", "evidence_id": "EV-SASBDB-SASDSD9", "mappings": [], "molecule_id": "P02925", "observable": { "type": "radius_of_gyration", "uncertainty": 0.003, "unit": "nm", "value": 2.123 }, "provenance": { "deposit_id": "SASDSD9", "doi": "10.1016/j.dib.2023.109932", "licence": "CC BY 4.0 (verify)", "retrieved": "2026-10-19", "source": "SASBDB", "url": "https://www.sasbdb.org/data/SASDSD9/" }, "reader": null, "source_kind": "deposit", "technique": "saxs_sans", "title": "SAXS/WAXS data of conformationally flexible ribose binding protein" }, { "conditions": { "applied_force_pn": null, "buffer": "50 mM Tris, 50 mM NaCl, 10% glycerol, 1 mM ribose", "environment": "in_vitro", "ions": [], "ligands": [ "partner: Ribose" ], "notes": "Other molecules in the sample are listed as partners; Rg is of the whole sample. Dmax 8.3 nm.", "ph": 7.0, "salt_mM": null, "temperature_c": 4.0 }, "construct": { "description": "Ribose import binding protein RbsB with Ribose", "labels": [] }, "data_format": "scattering curve", "data_level": "processed", "data_link": "https://www.sasbdb.org/data/SASDSE9/", "evidence_id": "EV-SASBDB-SASDSE9", "mappings": [], "molecule_id": "P02925", "observable": { "type": "radius_of_gyration", "uncertainty": 0.002, "unit": "nm", "value": 2.04 }, "provenance": { "deposit_id": "SASDSE9", "doi": "10.1016/j.dib.2023.109932", "licence": "CC BY 4.0 (verify)", "retrieved": "2026-10-19", "source": "SASBDB", "url": "https://www.sasbdb.org/data/SASDSE9/" }, "reader": null, "source_kind": "deposit", "technique": "saxs_sans", "title": "SAXS/WAXS data of conformationally flexible ribose binding protein" }, { "conditions": { "applied_force_pn": null, "buffer": "50 mM Tris, 50 mM NaCl, 10% glycerol, 1 mM ribose", "environment": "in_vitro", "ions": [], "ligands": [ "partner: Ribose" ], "notes": "Other molecules in the sample are listed as partners; Rg is of the whole sample. Dmax 7.6 nm.", "ph": 7.0, "salt_mM": null, "temperature_c": 4.0 }, "construct": { "description": "Ribose import binding protein RbsB with Ribose", "labels": [] }, "data_format": "scattering curve", "data_level": "processed", "data_link": "https://www.sasbdb.org/data/SASDSF9/", "evidence_id": "EV-SASBDB-SASDSF9", "mappings": [], "molecule_id": "P02925", "observable": { "type": "radius_of_gyration", "uncertainty": 0.003, "unit": "nm", "value": 2.046 }, "provenance": { "deposit_id": "SASDSF9", "doi": "10.1016/j.dib.2023.109932", "licence": "CC BY 4.0 (verify)", "retrieved": "2026-10-19", "source": "SASBDB", "url": "https://www.sasbdb.org/data/SASDSF9/" }, "reader": null, "source_kind": "deposit", "technique": "saxs_sans", "title": "SAXS/WAXS data of conformationally flexible ribose binding protein" }, { "conditions": { "applied_force_pn": null, "buffer": "50 mM Tris, 50 mM NaCl, 10% glycerol, 1 mM ribose", "environment": "in_vitro", "ions": [], "ligands": [ "partner: Ribose" ], "notes": "Other molecules in the sample are listed as partners; Rg is of the whole sample. Dmax 7.4 nm.", "ph": 7.0, "salt_mM": null, "temperature_c": 4.0 }, "construct": { "description": "Ribose import binding protein RbsB with Ribose", "labels": [] }, "data_format": "scattering curve", "data_level": "processed", "data_link": "https://www.sasbdb.org/data/SASDSG9/", "evidence_id": "EV-SASBDB-SASDSG9", "mappings": [], "molecule_id": "P02925", "observable": { "type": "radius_of_gyration", "uncertainty": 0.004, "unit": "nm", "value": 2.078 }, "provenance": { "deposit_id": "SASDSG9", "doi": "10.1016/j.dib.2023.109932", "licence": "CC BY 4.0 (verify)", "retrieved": "2026-10-19", "source": "SASBDB", "url": "https://www.sasbdb.org/data/SASDSG9/" }, "reader": null, "source_kind": "deposit", "technique": "saxs_sans", "title": "SAXS/WAXS data of conformationally flexible ribose binding protein" }, { "conditions": { "applied_force_pn": null, "buffer": "50 mM Tris, 50 mM NaCl, 10% glycerol", "environment": "in_vitro", "ions": [], "ligands": [], "notes": "Other molecules in the sample are listed as partners; Rg is of the whole sample. Dmax 12 nm.", "ph": 7.0, "salt_mM": null, "temperature_c": 22.0 }, "construct": { "description": "Ribose import binding protein RbsB", "labels": [] }, "data_format": "scattering curve", "data_level": "processed", "data_link": "https://www.sasbdb.org/data/SASDTB2/", "evidence_id": "EV-SASBDB-SASDTB2", "mappings": [], "molecule_id": "P02925", "observable": { "type": "radius_of_gyration", "uncertainty": 0.201, "unit": "nm", "value": 2.465 }, "provenance": { "deposit_id": "SASDTB2", "doi": "10.1016/j.dib.2023.109932", "licence": "CC BY 4.0 (verify)", "retrieved": "2026-10-19", "source": "SASBDB", "url": "https://www.sasbdb.org/data/SASDTB2/" }, "reader": null, "source_kind": "deposit", "technique": "saxs_sans", "title": "SAXS/WAXS data of conformationally flexible ribose binding protein" }, { "conditions": { "applied_force_pn": null, "buffer": "50 mM Tris, 50 mM NaCl, 10% glycerol, 1 mM ribose", "environment": "in_vitro", "ions": [], "ligands": [ "partner: Ribose" ], "notes": "Other molecules in the sample are listed as partners; Rg is of the whole sample. Dmax 12 nm.", "ph": 7.0, "salt_mM": null, "temperature_c": 22.0 }, "construct": { "description": "Ribose import binding protein RbsB with Ribose", "labels": [] }, "data_format": "scattering curve", "data_level": "processed", "data_link": "https://www.sasbdb.org/data/SASDTC2/", "evidence_id": "EV-SASBDB-SASDTC2", "mappings": [], "molecule_id": "P02925", "observable": { "type": "radius_of_gyration", "uncertainty": 0.185, "unit": "nm", "value": 2.241 }, "provenance": { "deposit_id": "SASDTC2", "doi": "10.1016/j.dib.2023.109932", "licence": "CC BY 4.0 (verify)", "retrieved": "2026-10-19", "source": "SASBDB", "url": "https://www.sasbdb.org/data/SASDTC2/" }, "reader": null, "source_kind": "deposit", "technique": "saxs_sans", "title": "SAXS/WAXS data of conformationally flexible ribose binding protein" }, { "conditions": { "applied_force_pn": null, "buffer": "Tris 50 mM, 50 mM NaCl, 10% glycerol, 5 mM ribose", "environment": "in_vitro", "ions": [], "ligands": [ "partner: Ribose" ], "notes": "Other molecules in the sample are listed as partners; Rg is of the whole sample. Dmax 10.7 nm.", "ph": 7.0, "salt_mM": null, "temperature_c": 22.0 }, "construct": { "description": "Ribose import binding protein RbsB with Ribose", "labels": [] }, "data_format": "scattering curve", "data_level": "processed", "data_link": "https://www.sasbdb.org/data/SASDTD2/", "evidence_id": "EV-SASBDB-SASDTD2", "mappings": [], "molecule_id": "P02925", "observable": { "type": "radius_of_gyration", "uncertainty": 0.182, "unit": "nm", "value": 1.919 }, "provenance": { "deposit_id": "SASDTD2", "doi": "10.1016/j.dib.2023.109932", "licence": "CC BY 4.0 (verify)", "retrieved": "2026-10-19", "source": "SASBDB", "url": "https://www.sasbdb.org/data/SASDTD2/" }, "reader": null, "source_kind": "deposit", "technique": "saxs_sans", "title": "SAXS/WAXS data of conformationally flexible ribose binding protein" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_silico", "ions": [], "ligands": [], "notes": "Computed prediction; no experimental conditions.", "ph": null, "salt_mM": null, "temperature_c": null }, "construct": { "description": "AlphaFold Monomer v2.0 pipeline, residues 1-296", "labels": [] }, "data_format": "mmCIF, PAE JSON", "data_level": "processed", "data_link": "https://alphafold.ebi.ac.uk/entry/P02925", "evidence_id": "EV-AFDB-AF-P02925-F1", "mappings": [], "molecule_id": "P02925", "observable": { "type": "plddt", "uncertainty": null, "unit": "pLDDT", "value": 94.5 }, "provenance": { "deposit_id": "AF-P02925-F1", "doi": null, "licence": "CC BY 4.0", "retrieved": "2026-10-19", "source": "AlphaFold DB", "url": "https://alphafold.ebi.ac.uk/entry/P02925" }, "reader": null, "source_kind": "computed", "technique": "af_prediction", "title": "AlphaFold DB prediction AF-P02925-F1" }, { "conditions": { "applied_force_pn": null, "buffer": null, "environment": "in_silico", "ions": [], "ligands": [], "notes": "Simulation; temperature is the thermostat setting.", "ph": null, "salt_mM": null, "temperature_c": 26.85 }, "construct": { "description": "start 2DRI; Amber Parm99", "labels": [] }, "data_format": "trajectory", "data_level": "processed", "data_link": "https://mmb.mddbr.eu/#/id/A00BA/overview", "evidence_id": "EV-MDDB-A00BA", "mappings": [], "molecule_id": "P02925", "observable": { "type": "trajectory", "uncertainty": null, "unit": "ns", "value": 10.0 }, "provenance": { "deposit_id": "A00BA", "doi": "10.1016/j.str.2010.07.013", "licence": "This trajectory dataset is released under a Creative Commons Attribution 4.0 International Public License", "retrieved": "2026-10-19", "source": "MDDB", "url": "https://mmb.mddbr.eu/#/id/A00BA/overview" }, "reader": null, "source_kind": "computed", "technique": "md", "title": "MoDEL 2DRI" } ], "models": [ { "assumptions": null, "basis": "observed", "constraints_used": [ "EV-PDB-1URP-1" ], "file": "models/P02925/RBP-open.cif", "format": "mmCIF", "model_id": "RBP-open-cif", "molecule_id": "P02925", "provenance": { "deposit_id": "1URP", "doi": "10.1006/jmbi.1998.1785", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://files.rcsb.org/download/1URP.cif" }, "state_id": "RBP-open" }, { "assumptions": null, "basis": "observed", "constraints_used": [ "EV-PDB-1URP-1" ], "file": "models/P02925/RBP-open.pdb", "format": "PDB", "model_id": "RBP-open-pdb", "molecule_id": "P02925", "provenance": { "deposit_id": "1URP", "doi": "10.1006/jmbi.1998.1785", "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://files.rcsb.org/download/1URP.pdb" }, "state_id": "RBP-open" }, { "assumptions": null, "basis": "observed", "constraints_used": [ "EV-PDB-2DRI-1" ], "file": "models/P02925/RBP-closed.cif", "format": "mmCIF", "model_id": "RBP-closed-cif", "molecule_id": "P02925", "provenance": { "deposit_id": "2DRI", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://files.rcsb.org/download/2DRI.cif" }, "state_id": "RBP-closed" }, { "assumptions": null, "basis": "observed", "constraints_used": [ "EV-PDB-2DRI-1" ], "file": "models/P02925/RBP-closed.pdb", "format": "PDB", "model_id": "RBP-closed-pdb", "molecule_id": "P02925", "provenance": { "deposit_id": "2DRI", "doi": null, "licence": "CC0 1.0 (wwPDB archive data)", "retrieved": "2026-10-19", "source": "RCSB PDB", "url": "https://files.rcsb.org/download/2DRI.pdb" }, "state_id": "RBP-closed" } ], "molecule": { "components": [], "domains": [], "gene": "rbsB", "identifiers": { "genbank": null, "isoform": null, "nakb": null, "pdb": [], "rfam": null, "rnacentral": null, "uniprot": "P02925" }, "ligands": [], "modifications": [], "molecule_id": "P02925", "molecule_type": "protein", "name": "Ribose import binding protein RbsB", "organism": { "name": "Escherichia coli (strain K12)", "taxon_id": 83333 }, "provenance": { "deposit_id": "P02925", "doi": null, "licence": "CC BY 4.0 (UniProt)", "retrieved": "2026-10-19", "source": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P02925/entry" }, "sequence": "MNMKKLATLVSAVALSATVSANAMAKDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQATKGEVVSHIASDNVLGGKIAGDYIAKKAGEGAKVIELQGIAGTSAARERGEGFQQAVAAHKFNVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDVMVVGFDGTPDGEKAVNDGKLAATIAQLPDQIGAKGVETADKVLKGEKVQAKYPVDLKLVVKQ", "sequence_length": 296 }, "molecule_id": "P02925", "states": [ { "assumptions": [], "basis": "observed", "description": "Ligand-free open form, as in 1URP.", "family_label": null, "molecule_id": "P02925", "name": "open, ligand-free", "parent_state": null, "population": null, "provenance": { "deposit_id": null, "doi": null, "licence": "Project licence (pending decision)", "retrieved": "2026-10-19", "source": "Conformome curation (P02925.yaml)", "url": "https://github.com/matth55/conformome/blob/HEAD/curation/P02925.yaml" }, "representative_model": "RBP-open-cif", "secondary_structure": null, "state_id": "RBP-open", "status": "draft" }, { "assumptions": [], "basis": "observed", "description": "Closed form with D-ribose bound, as in 2DRI.", "family_label": null, "molecule_id": "P02925", "name": "closed, ribose-bound", "parent_state": null, "population": null, "provenance": { "deposit_id": null, "doi": null, "licence": "Project licence (pending decision)", "retrieved": "2026-10-19", "source": "Conformome curation (P02925.yaml)", "url": "https://github.com/matth55/conformome/blob/HEAD/curation/P02925.yaml" }, "representative_model": "RBP-closed-cif", "secondary_structure": null, "state_id": "RBP-closed", "status": "draft" } ], "transitions": [] }