MolNFT v1 · #169858 · protein
Nucleoside diphosphate kinase from aspergillus fumgiatus AF293 bound to ADP
6XP7: “Nucleoside diphosphate kinase from aspergillus fumgiatus AF293 bound to ADP”. X-ray diffraction, 1 ligand (ADP), 6 pockets (best druggability 0.63). MolNFT v1 #169858 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6XP7
- Type
- protein
- Length
- 456 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- Q7Z8P9
- Ligands
- ADP
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 152 | 48% helix, 16% strand | Q7Z8P9 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.63 | 0.83 | 31 | empty |
| 2 | 90 | 0.53 | 0.84 | 22 | empty |
| 3 | 147 | 0.47 | 0.77 | 23 | ADP |
| 4 | 168 | 0.46 | 0.76 | 27 | ADP |
| 5 | 158 | 0.45 | 0.75 | 27 | ADP |
Interfaces
2 interfaces between chains.
- A–B · 989 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 816 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6XP7 · Nucleoside Diphosphate Kinase from Aspergillus fumgiatus Af293 bound to ADP · the same entry in another collection · chain A against A, TM-score 1.00
- Q7Z8P9 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase (Q7Z8P9) · 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 Q7Z8P9
- Elsewhere: RCSB PDB 6XP7 · PDBe 6XP7 · UniProt Q7Z8P9
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