Research workbench
Nucleoside diphosphate kinase from aspergillus fumgiatus AF293 bound to dtdp
Analyse Nucleoside diphosphate kinase from aspergillus fumgiatus AF293 bound to dtdp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XPV
- Type
- protein
- Length
- 922 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
- Ligands
- TYD
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, G | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 154 | 45% helix, 16% strand | Q7Z8P9 |
| C, H | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 153 | 47% helix, 16% strand | Q7Z8P9 |
Ligands and binding sites
- TYD · Thymidine-5'-diphosphate · ligand · 6 copies · chains A, B, C, E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1131 | 0.83 | 0.84 | 111 | empty |
| 2 | 383 | 0.80 | 0.89 | 50 | empty |
| 3 | 385 | 0.80 | 0.89 | 51 | empty |
| 4 | 200 | 0.50 | 0.76 | 28 | TYD |
| 5 | 195 | 0.49 | 0.76 | 28 | TYD |
Interfaces
12 interfaces between chains.
- E–G · 987 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 986 Ų buried · 11 hydrogen bonds · protein-protein
- C–H · 974 Ų buried · 13 hydrogen bonds · protein-protein
- A–H · 852 Ų buried · 15 hydrogen bonds · protein-protein
- A–G · 851 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6XPV · Nucleoside Diphosphate Kinase from Aspergillus fumgiatus Af293 bound to dTDP · the same entry in another collection · chain H against H, TM-score 1.00
- Q7Z8P9 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase (Q7Z8P9) · a predicted model of the same protein · chain C 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 6XPV · PDBe 6XPV · UniProt Q7Z8P9
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