Adenylate kinase
UniProt P69441 · gene adk · Escherichia coli (strain K12) · 214 residues
31evidence items
19mapped to a state
2states
3techniques
3sources
0conflicts
Coverage grid
Mapped evidence per state and technique. Shaded rows rest on a single technique. Badge = best data level in the cell: raw (traces, images, FIDs: can be re-analysed), proc (maps, curves, tables, trajectories) or rep (values in the paper only).
| State | Basis | xray | force_spectroscopy | af_prediction | Total |
|---|---|---|---|---|---|
| open (apo) ADK-open | observed (one method) | proc 3 | · | · | 3 |
| closed (Ap5A-bound) ADK-closed | observed (one method) | proc 16 | · | · | 16 |
Unmapped evidence: 12 of 31 items. Mappings come from curator assignments and curated rules; see About for how rules work.
Sources
| Source | Evidence | Mapped |
|---|---|---|
| AlphaFold DB | 1 | 0 |
| RCSB PDB | 29 | 19 |
| SMASH-BIO | 1 | 0 |
Curated rules applied
adk-ap5a-closed: 15 itemsadk-apo-open: 2 items
Structure
Choose a state. Each model is badged observed or inferred; assumptions are one click away.
States and transitions
| State | Basis | Parent | Description |
|---|---|---|---|
| open (apo) ADK-open | observed | — | Apo enzyme with the LID and NMP domains in the open arrangement, as in 4AKE. Domain definitions to be confirmed by the curator. |
| closed (Ap5A-bound) ADK-closed | observed | — | LID and NMP domains closed around the bisubstrate inhibitor Ap5A, as in 1AKE. |
No transitions recorded in this version (no rate or free-energy evidence has been curated yet).
Evidence
One row per deposit or experiment. Filter by technique, environment or text. Unmapped evidence is listed too.
| Evidence | Technique | Observable | Conditions | Mapped to state |
|---|---|---|---|---|
| EV-PDB-1AKE-1 RCSB PDB | xray | resolution: 2 Å | in vitro · ligands AP5 STRUCTURE OF THE COMPLEX BETWEEN ADENYLATE KINASE FROM ESCHERICHIA COLI AND THE INHIBITOR AP5A REFINED AT 1.9 ANGSTROMS RESOLUTION: A MODEL FOR A CATALYTIC TRANSITION STATE · ADENYLATE KINASE (chains A,B) | closed (Ap5A-bound) · curator:draft (unreviewed) · high Ap5A-bound structure with closed LID and NMP domains; representative for ADK-closed. |
| EV-PDB-1E4V-1 RCSB PDB | xray | resolution: 1.85 Å | in vitro · 5.85 °C · pH 6.7 · ligands AP5 Mutant G10V of adenylate kinase from E. coli, modified in the Gly-loop · Adenylate kinase (chains A,B) | closed (Ap5A-bound) · rule:adk-ap5a-closed · medium Bisubstrate inhibitor Ap5A (AP5) bound; it closes the LID and NMP domains. |
| EV-PDB-1E4Y-1 RCSB PDB | xray | resolution: 1.85 Å | in vitro · 5.85 °C · pH 7.2 · ligands AP5 Mutant P9L of adenylate kinase from E. coli, modified in the Gly-loop · Adenylate kinase (chains A,B) | closed (Ap5A-bound) · rule:adk-ap5a-closed · medium Bisubstrate inhibitor Ap5A (AP5) bound; it closes the LID and NMP domains. |
| EV-PDB-2ECK-1 RCSB PDB | xray | resolution: 2.8 Å | in vitro · 19.85 °C · pH 6.7 · ligands ADP, AMP STRUCTURE OF PHOSPHOTRANSFERASE · ADENYLATE KINASE (chains A,B) | unmapped |
| EV-PDB-3HPQ-1 RCSB PDB | xray | resolution: 2 Å | in vitro · -173.15 °C · ligands AP5 Crystal structure of wild-type adenylate kinase from E. coli, in complex with Ap5A · Adenylate kinase (chains A,B) | closed (Ap5A-bound) · rule:adk-ap5a-closed · medium Bisubstrate inhibitor Ap5A (AP5) bound; it closes the LID and NMP domains. |
| EV-PDB-3HPR-1 RCSB PDB | xray | resolution: 2 Å | in vitro · -173.15 °C · ligands AP5 Crystal structure of V148G adenylate kinase from E. coli, in complex with Ap5A · Adenylate kinase (chains A,B) | closed (Ap5A-bound) · rule:adk-ap5a-closed · medium Bisubstrate inhibitor Ap5A (AP5) bound; it closes the LID and NMP domains. |
| EV-PDB-4AKE-1 RCSB PDB | xray | resolution: 2.2 Å | in vitro ADENYLATE KINASE · ADENYLATE KINASE (chains A,B) | open (apo) · curator:draft (unreviewed) · high Apo structure with open LID and NMP domains; representative for ADK-open. Domain assignment to be confirmed by the curator. |
| EV-PDB-4X8L-1 RCSB PDB | xray | resolution: 1.7 Å | in vitro · -173.15 °C · pH 8.5 · ligands AP5, MG, NA Crystal structure of E. coli Adenylate kinase P177A mutant in complex with inhibitor Ap5a · Adenylate kinase (chains A,B) | closed (Ap5A-bound) · rule:adk-ap5a-closed · medium Bisubstrate inhibitor Ap5A (AP5) bound; it closes the LID and NMP domains. |
| EV-PDB-4X8M-1 RCSB PDB | xray | resolution: 2.6 Å | in vitro · -173.15 °C · pH 8 Crystal structure of E. coli Adenylate kinase Y171W mutant · Adenylate kinase (chains A) | open (apo) · rule:adk-apo-open · low Crystal structure with no ligand; apo E. coli ADK crystallises open, but this is not checked per entry. |
| EV-PDB-4X8O-1 RCSB PDB | xray | resolution: 2.1 Å | in vitro · -173.15 °C · pH 6 · ligands AP5, MG, NA Crystal structure of E. coli Adenylate kinase Y171W mutant in complex with inhibitor Ap5a · Adenylate kinase (chains A,B) | closed (Ap5A-bound) · rule:adk-ap5a-closed · medium Bisubstrate inhibitor Ap5A (AP5) bound; it closes the LID and NMP domains. |
| EV-PDB-5EJE-1 RCSB PDB | xray | resolution: 1.9 Å | in vitro · -173.15 °C · pH 5.8 · ligands AP5, CO Crystal structure of E. coli Adenylate kinase G56C/T163C double mutant in complex with Ap5a · Adenylate kinase (chains A,B) | closed (Ap5A-bound) · rule:adk-ap5a-closed · medium Bisubstrate inhibitor Ap5A (AP5) bound; it closes the LID and NMP domains. |
| EV-PDB-6F7U-1 RCSB PDB | xray | resolution: 1.4 Å | in vitro · -173.15 °C · pH 6.5 · ligands GCP, MG Molecular Mechanism of ATP versus GTP Selectivity of Adenylate Kinase · Adenylate kinase (chains A) | unmapped |
| EV-PDB-6RZE-1 RCSB PDB | xray | resolution: 1.69 Å | in vitro · -173.15 °C · pH 8.5 · ligands CL, NA Crystal structure of E. coli Adenylate kinase R119A mutant · Adenylate kinase (chains A) | unmapped |
| EV-PDB-6S36-1 RCSB PDB | xray | resolution: 1.6 Å | in vitro · -173.15 °C · pH 8.5 · ligands CL, MG, NA Crystal structure of E. coli Adenylate kinase R119K mutant · Adenylate kinase (chains A) | unmapped |
| EV-PDB-7APU-1 RCSB PDB | xray | resolution: 1.36 Å | in vitro · -173.15 °C · pH 4.6 · ligands ADP, NA Structure of Adenylate kinase from Escherichia coli in complex with two ADP molecules refined at 1.36 A resolution. · Adenylate kinase (chains A,B) | unmapped |
| EV-PDB-8BQF-1 RCSB PDB | xray | resolution: 2.05 Å | in vitro · -173.15 °C · pH 7 · ligands AP5 Adenylate Kinase L107I MUTANT · Adenylate kinase (chains A,B,C,D,E,F) | closed (Ap5A-bound) · rule:adk-ap5a-closed · medium Bisubstrate inhibitor Ap5A (AP5) bound; it closes the LID and NMP domains. |
| EV-PDB-8CRG-1 RCSB PDB | xray | resolution: 1.49 Å | in vitro · -173.15 °C · pH 6.5 · ligands ADP, MPO E. coli adenylate kinase in complex with two ADP molecules as a result of enzymatic AP4A hydrolysis · Adenylate kinase (chains A,B) | unmapped |
| EV-PDB-8Q2B-1 RCSB PDB | xray | resolution: 1.76 Å | in vitro · -173.15 °C · pH 6.5 · ligands AP5, MPO, SO4 E. coli Adenylate Kinase variant D158A (AK D158A) showing significant changes to the stacking of catalytic arginine side chains · Adenylate kinase (chains A,B) | closed (Ap5A-bound) · rule:adk-ap5a-closed · medium Bisubstrate inhibitor Ap5A (AP5) bound; it closes the LID and NMP domains. |
| EV-PDB-8RJ4-1 RCSB PDB | xray | resolution: 2.11 Å | in vitro · -173.15 °C · pH 6.4 · ligands ADP, CL, MG E. coli adenylate kinase in complex with two ADP molecules and Mg2+ as a result of enzymatic AP4A hydrolysis · Adenylate kinase (chains A,B,C,D) | unmapped |
| EV-PDB-8RJ6-1 RCSB PDB | xray | resolution: 1.9 Å | in vitro · -173.15 °C · pH 7 · ligands ADP, AMP, ATP, MG E. coli adenylate kinase in complex with ATP and AMP and Mg2+ as a result of enzymatic AP4A hydrolysis. · Adenylate kinase (chains A,B) | unmapped |
| EV-PDB-8RJ9-1 RCSB PDB | xray | resolution: 1.59 Å | in vitro · -173.15 °C · ligands ADP E. coli adenylate kinase Asp84Ala variant in complex with two ADP molecules as a result of enzymatic AP4A hydrolysis. · Adenylate kinase (chains A,B) | unmapped |
| EV-PDB-9R6U-1 RCSB PDB | xray | resolution: 1.77 Å | in vitro · -173.15 °C · pH 5.4 · ligands AP5, GOL, NA Crystal structure of E. coli Adenylate kinase K47A mutant in complex with inhibitor Ap5A · Adenylate kinase (chains A,B) | closed (Ap5A-bound) · rule:adk-ap5a-closed · medium Bisubstrate inhibitor Ap5A (AP5) bound; it closes the LID and NMP domains. |
| EV-PDB-9R71-1 RCSB PDB | xray | resolution: 1.61 Å | in vitro · -173.15 °C · ligands AP5 Crystal structure of E. coli Adenylate kinase E114A mutant in complex with inhibitor Ap5a. · Adenylate kinase (chains A,B) | closed (Ap5A-bound) · rule:adk-ap5a-closed · medium Bisubstrate inhibitor Ap5A (AP5) bound; it closes the LID and NMP domains. |
| EV-PDB-9L14-1 RCSB PDB | xray | resolution: 1.86 Å | in vitro · -173.15 °C · ligands AP5, MG Crystal structure of the monobody CL-1 in complex with the Escherichia coli adenylate kinase · Adenylate kinase (chains A) | closed (Ap5A-bound) · rule:adk-ap5a-closed · medium Bisubstrate inhibitor Ap5A (AP5) bound; it closes the LID and NMP domains. |
| EV-PDB-8PVW-1 RCSB PDB | xray | resolution: 2 Å | in vitro · -173.15 °C · pH 8 · ligands AP5 Structure of a short E. coli adenylate kinase in complex with Ap5A · Adenylate kinase (chains A) | closed (Ap5A-bound) · rule:adk-ap5a-closed · medium Bisubstrate inhibitor Ap5A (AP5) bound; it closes the LID and NMP domains. |
| EV-PDB-6HAP-1 RCSB PDB | xray | resolution: 2.7 Å | in vitro · -173.15 °C · pH 5.5 · ligands AP5 Adenylate kinase · Adenylate kinase (chains A) | closed (Ap5A-bound) · rule:adk-ap5a-closed · medium Bisubstrate inhibitor Ap5A (AP5) bound; it closes the LID and NMP domains. |
| EV-PDB-6HAM-1 RCSB PDB | xray | resolution: 2.55 Å | in vitro · -173.15 °C · pH 8 · ligands AP5 Adenylate kinase · Adenylate kinase (chains A) | closed (Ap5A-bound) · rule:adk-ap5a-closed · medium Bisubstrate inhibitor Ap5A (AP5) bound; it closes the LID and NMP domains. |
| EV-PDB-4X8H-1 RCSB PDB | xray | resolution: 2.5 Å | in vitro · -173.15 °C · pH 8.5 Crystal structure of E. coli Adenylate kinase P177A mutant · Adenylate kinase (chains A) | open (apo) · rule:adk-apo-open · low Crystal structure with no ligand; apo E. coli ADK crystallises open, but this is not checked per entry. |
| EV-PDB-1ANK-1 RCSB PDB | xray | resolution: 2 Å | in vitro · ligands AMP, ANP THE CLOSED CONFORMATION OF A HIGHLY FLEXIBLE PROTEIN: THE STRUCTURE OF E. COLI ADENYLATE KINASE WITH BOUND AMP AND AMPPNP · ADENYLATE KINASE (chains A,B) | unmapped |
| EV-AFDB-AF-P69441-F1 AlphaFold DB | af_prediction | plddt: 95.94 pLDDT | in silico AlphaFold DB prediction AF-P69441-F1 · AlphaFold Monomer v2.0 pipeline, residues 1-214 | unmapped |
| EV-SMASH-SMFS-004075 SMASH-BIO | force_spectroscopy | study_record | in vitro · pH 7.5 Subnanometre enzyme mechanics probed by single-molecule force spectroscopy. · Adenylate kinase; optical tweezers; experiment class: unfolding_protein | unmapped |
Conflicts
No conflicts found among comparable evidence.
31 evidence items could not be compared: they lack a comparable observable type, a value, or an uncertainty. Absence of a conflict here is not agreement.
Downloads
- Protein bundle (JSON)
- ADK-open-cif (mmCIF, observed)
- ADK-open-pdb (PDB, observed)
- ADK-closed-cif (mmCIF, observed)
- ADK-closed-pdb (PDB, observed)
- Curation file (YAML)