MolNFT v1 · #887 · protein
Structure of the complex between adenylate kinase from escherichia COLI and the inhibitor AP5A refined at 1.9 ångströms resolution: a model for a catalytic transition state
1AKE: “Structure of the complex between adenylate kinase from escherichia COLI and the inhibitor AP5A refined at 1.9…”. X-ray diffraction, 1 ligand (AP5), 5 pockets (best druggability 0.84). MolNFT v1 #887 on GenesisL1: 3D structure…
- PDB
- 1AKE
- Type
- protein
- Length
- 428 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinase
- EC
- 2.7.4.3
- UniProt
- P69441
- Ligands
- AP5
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenylate kinase (EC 2.7.4.3) | protein | 214 | 49% helix, 17% strand | P69441 |
Ligands and binding sites
- AP5 · Bis(adenosine)-5'-pentaphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 467 | 0.84 | 0.91 | 64 | AP5 |
| 2 | 453 | 0.83 | 0.90 | 61 | AP5 |
| 3 | 50 | 0.41 | 0.82 | 12 | empty |
| 4 | 75 | 0.31 | 0.74 | 15 | empty |
| 5 | 74 | 0.30 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 254 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1AKE · Structure of the complex between adenylate kinase from escherichia COLI and the inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- P69441 · AlphaFold monomer V2.0 prediction for adenylate kinase (P69441) · a predicted model of the same protein · chain A against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P69441
- Elsewhere: RCSB PDB 1AKE · PDBe 1AKE · UniProt P69441
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