MolNFT v1 · #83919 · protein
Purification, characterization and structure of nucleoside diphosphate kinase from drosophila S2 cells
3WX8: “Purification, characterization and structure of nucleoside diphosphate kinase from drosophila S2 cells”. X-ray diffraction, 7 pockets (best druggability 0.61). MolNFT v1 #83919 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3WX8
- Type
- protein
- Length
- 458 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
- P08879
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 153 | 49% helix, 14% strand | P08879 |
| C | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 152 | 49% helix, 14% strand | P08879 |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 313 | 0.61 | 0.79 | 24 | empty |
| 2 | 207 | 0.50 | 0.76 | 32 | empty |
| 3 | 153 | 0.46 | 0.76 | 27 | empty |
| 4 | 175 | 0.44 | 0.74 | 25 | empty |
| 5 | 95 | 0.42 | 0.78 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 921 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 906 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 892 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3WX8 · Purification, characterization and structure of nucleoside diphosphate kinase from… · the same entry in another collection · chain A against A, TM-score 1.00
- P08879 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase (P08879) · 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 P08879
- Elsewhere: RCSB PDB 3WX8 · PDBe 3WX8 · UniProt P08879
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