Research workbench
E134A mutant nucleoside diphosphate kinase derived from halomonas sp. 593
Analyse E134A mutant nucleoside diphosphate kinase derived from halomonas sp. 593 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VGU
- Type
- protein
- Length
- 1,118 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- Q83WH5
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 140 | 46% helix, 20% strand | Q83WH5 |
| H | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 138 | 43% helix, 22% strand | Q83WH5 |
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.84 | 0.85 | 75 | empty |
| 2 | 1082 | 0.82 | 0.83 | 87 | empty |
| 3 | 149 | 0.79 | 0.96 | 25 | empty |
| 4 | 55 | 0.73 | 0.99 | 16 | empty |
| 5 | 165 | 0.51 | 0.78 | 23 | empty |
Interfaces
16 interfaces between chains.
- C–G · 888 Ų buried · 22 hydrogen bonds · protein-protein
- D–H · 879 Ų buried · 24 hydrogen bonds · protein-protein
- A–E · 873 Ų buried · 18 hydrogen bonds · protein-protein
- B–F · 866 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 553 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3VGU · 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 3VGU · PDBe 3VGU · UniProt Q83WH5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.