MolNFT v1 · #109634 · protein
Crystal structure of E. COLI adenylate kinase Y171W mutant in complex with inhibitor AP5A
4X8O: “Crystal structure of E. COLI adenylate kinase Y171W mutant in complex with inhibitor AP5A”. X-ray diffraction, 3 ligands (AP5, MG, NA), 4 pockets (best druggability 0.82). MolNFT v1 #109634 on GenesisL1: 3D structure, binding sites…
- PDB
- 4X8O
- 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, MG, NA
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenylate kinase (EC 2.7.4.3) | protein | 214 | 46% helix, 17% strand | P69441 |
Ligands and binding sites
- AP5 · Bis(adenosine)-5'-pentaphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.82 | 0.88 | 64 | AP5, MG |
| 2 | 519 | 0.82 | 0.88 | 68 | AP5, MG |
| 3 | 167 | 0.46 | 0.75 | 17 | empty |
| 4 | 50 | 0.31 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 348 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4X8O · Crystal structure of E. coli Adenylate kinase Y171W mutant in complex with inhibitor Ap5a · 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 0.99
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 4X8O · PDBe 4X8O · UniProt P69441
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