Research workbench
Crystal structure of staphylococcus aureus nucleoside diphosphate kinase complexed with ADP and vanadate
Analyse Crystal structure of staphylococcus aureus nucleoside diphosphate kinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q8Y
- Type
- protein
- Length
- 1,192 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
- Q5HFV4
- Ligands
- ADP, MG, VO4
- Pockets
- 12 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 149 | 44% helix, 16% strand | Q5HFV4 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B, D, E, G, H
- MG · Magnesium ion · metal · 4 copies · chains D, H
- VO4 · Vanadate ion · ion · 8 copies · chains A, B, C, D, E, F, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.87 | 0.88 | 78 | empty |
| 2 | 779 | 0.73 | 0.79 | 63 | ADP, VO4, MG |
| 3 | 229 | 0.54 | 0.77 | 33 | ADP, VO4 |
| 4 | 169 | 0.53 | 0.79 | 23 | VO4 |
| 5 | 213 | 0.53 | 0.77 | 27 | ADP, VO4 |
Interfaces
18 interfaces between chains.
- C–G · 1062 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 1054 Ų buried · 24 hydrogen bonds · protein-protein
- B–F · 1052 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 869 Ų buried · 13 hydrogen bonds · protein-protein
- E–G · 862 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3Q8Y · Crystal structure of Staphylococcus aureus nucleoside diphosphate kinase complexed with… · the same entry in another collection · chain H against H, TM-score 1.00
- Q5HFV4 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase (Q5HFV4) · a predicted model of the same protein · chain A 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 Q5HFV4
- Elsewhere: RCSB PDB 3Q8Y · PDBe 3Q8Y · UniProt Q5HFV4
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