MolNFT v1 · #173129 · protein
Structure of adenylate kinase from escherichia COLI in complex with two ADP molecules refined at 1.36 a resolution.
7APU: “Structure of adenylate kinase from escherichia COLI in complex with two ADP molecules refined at 1.36 a…”. X-ray diffraction, 2 ligands (ADP, NA), 4 pockets (best druggability 0.82). MolNFT v1 #173129 on GenesisL1: 3D structure…
- PDB
- 7APU
- 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
- ADP, NA
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenylate kinase (EC 2.7.4.3) | protein | 214 | 48% helix, 16% strand | P69441 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
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 | 580 | 0.82 | 0.87 | 73 | ADP |
| 2 | 518 | 0.81 | 0.87 | 65 | ADP |
| 3 | 156 | 0.46 | 0.76 | 18 | empty |
| 4 | 69 | 0.38 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 400 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7APU · Structure of Adenylate kinase from Escherichia coli in complex with two ADP molecules… · 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 7APU · PDBe 7APU · UniProt P69441
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