MolNFT v1 · #87912 · protein
Crystal structure of adenylate kinase from aquifex aeolicus with mgadp bound
4CF7: “Crystal structure of adenylate kinase from aquifex aeolicus with mgadp bound”. X-ray diffraction, 3 ligands (ADP, AMP, MG), 6 pockets (best druggability 0.84). MolNFT v1 #87912 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4CF7
- Type
- protein
- Length
- 406 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinase
- EC
- 2.7.4.3
- UniProt
- O66490
- Ligands
- ADP, AMP, MG
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenylate kinase (EC 2.7.4.3) | protein | 203 | 52% helix, 16% strand | O66490 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B
- AMP · Adenosine monophosphate · ligand · chains B
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1059 | 0.84 | 0.85 | 85 | ADP |
| 2 | 450 | 0.80 | 0.88 | 55 | ADP, AMP, MG |
| 3 | 130 | 0.52 | 0.81 | 20 | empty |
| 4 | 58 | 0.43 | 0.82 | 9 | empty |
| 5 | 82 | 0.41 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 700 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4CF7 · Crystal structure of adenylate kinase from Aquifex aeolicus with MgADP bound · the same entry in another collection · chain A against A, TM-score 1.00
- O66490 · AlphaFold monomer V2.0 prediction for adenylate kinase (O66490) · 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 O66490
- Elsewhere: RCSB PDB 4CF7 · PDBe 4CF7 · UniProt O66490
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