MolNFT v1 · #169879 · protein
Nucleoside diphosphate kinase from aspergillus fumgiatus AF293 bound to GDP
6XPS: “Nucleoside diphosphate kinase from aspergillus fumgiatus AF293 bound to GDP”. X-ray diffraction, 2 ligands (GDP, MG), 7 pockets (best druggability 0.63). MolNFT v1 #169879 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6XPS
- Type
- protein
- Length
- 459 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
- GDP, MG
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 153 | 47% helix, 16% strand | Q7Z8P9 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.63 | 0.83 | 31 | empty |
| 2 | 86 | 0.52 | 0.84 | 23 | empty |
| 3 | 181 | 0.49 | 0.77 | 27 | GDP, MG |
| 4 | 191 | 0.48 | 0.76 | 27 | GDP, MG |
| 5 | 145 | 0.45 | 0.76 | 26 | GDP, MG |
Interfaces
2 interfaces between chains.
- A–B · 989 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 854 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6XPS · Nucleoside Diphosphate Kinase from Aspergillus fumgiatus Af293 bound to GDP · 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 6XPS · PDBe 6XPS · UniProt Q7Z8P9
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