Research workbench
Crystal structure of staphylococcus aureus nucleoside diphosphate kinase complexed with ADP
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
- 3Q8U
- Type
- protein
- Length
- 894 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
- Q5HFV4
- Ligands
- ADP, MG
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 149 | 44% helix, 17% strand | Q5HFV4 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 5 copies · chains A, B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 956 | 0.86 | 0.88 | 87 | empty |
| 2 | 182 | 0.55 | 0.80 | 29 | ADP, MG |
| 3 | 222 | 0.53 | 0.77 | 30 | ADP, MG |
| 4 | 194 | 0.52 | 0.78 | 29 | ADP, MG |
| 5 | 200 | 0.52 | 0.77 | 28 | ADP |
Interfaces
15 interfaces between chains.
- E–F · 1049 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1044 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1041 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 937 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 911 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3Q8U · Crystal structure of Staphylococcus aureus nucleoside diphosphate kinase complexed with… · the same entry in another collection · chain C against C, 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 3Q8U · PDBe 3Q8U · UniProt Q5HFV4
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