Research workbench
Nucleoside diphosphate kinase from aspergillus fumgiatus AF293
Analyse Nucleoside diphosphate kinase from aspergillus fumgiatus AF293 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XP4
- Type
- protein
- Length
- 929 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- Q7Z8P9
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 156 | 46% helix, 15% strand | Q7Z8P9 |
| B | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 157 | 46% helix, 15% strand | Q7Z8P9 |
| C | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 155 | 46% helix, 15% strand | Q7Z8P9 |
| D | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 154 | 47% helix, 16% strand | Q7Z8P9 |
| E | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 154 | 47% helix, 16% strand | Q7Z8P9 |
| F | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 153 | 48% helix, 16% strand | Q7Z8P9 |
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.78 | 0.83 | 68 | empty |
| 2 | 351 | 0.76 | 0.86 | 64 | empty |
| 3 | 986 | 0.72 | 0.76 | 97 | empty |
| 4 | 93 | 0.52 | 0.83 | 21 | empty |
| 5 | 107 | 0.49 | 0.80 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–C · 990 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 982 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 856 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 774 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 143 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6XP4 · Nucleoside Diphosphate Kinase from Aspergillus fumgiatus Af293 · the same entry in another collection · chain F against F, TM-score 1.00
- Q7Z8P9 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase (Q7Z8P9) · a predicted model of the same protein · chain F against A, TM-score 0.98
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 6XP4 · PDBe 6XP4 · UniProt Q7Z8P9
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