MolNFT v1 · #82250 · protein
E134A mutant nucleoside diphosphate kinase derived from halomonas sp. 593
3VGV: “E134A mutant nucleoside diphosphate kinase derived from halomonas sp. 593”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #82250 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3VGV
- Type
- protein
- Length
- 2,193 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- Q83WH5
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 136 | 43% helix, 21% strand | Q83WH5 |
| B, C, E, F, G, H, I, K, L, M, P | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 140 | 46% helix, 20% strand | Q83WH5 |
| D | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 137 | 45% helix, 20% strand | Q83WH5 |
| J | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 129 | 48% helix, 21% strand | Q83WH5 |
| N | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 113 | 43% helix, 22% strand | Q83WH5 |
| O | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 138 | 38% helix, 20% strand | Q83WH5 |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 994 | 0.84 | 0.85 | 86 | empty |
| 2 | 1052 | 0.84 | 0.85 | 81 | empty |
| 3 | 986 | 0.83 | 0.84 | 80 | empty |
| 4 | 969 | 0.83 | 0.85 | 81 | empty |
| 5 | 175 | 0.80 | 0.95 | 26 | empty |
Interfaces
37 interfaces between chains.
- A–B · 914 Ų buried · 23 hydrogen bonds · protein-protein
- M–N · 905 Ų buried · 21 hydrogen bonds · protein-protein
- O–P · 897 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 896 Ų buried · 19 hydrogen bonds · protein-protein
- K–L · 890 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3VGV · E134A mutant nucleoside diphosphate kinase derived from Halomonas sp. 593 · the same entry in another collection · chain A against A, TM-score 1.00
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 Q83WH5
- Elsewhere: RCSB PDB 3VGV · PDBe 3VGV · UniProt Q83WH5
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