Research workbench
S120G mutant of human nucleoside diphosphate kinase a complexed with ADP
Analyse S120G mutant of human nucleoside diphosphate kinase a complexed with ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HVE
- Type
- protein
- Length
- 453 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase a
- EC
- 2.7.4.6
- UniProt
- P15531
- Ligands
- ADP
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Nucleoside diphosphate kinase a (EC 2.7.4.6) | protein | 151 | 43% helix, 16% strand | P15531 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.68 | 0.83 | 39 | empty |
| 2 | 354 | 0.60 | 0.77 | 55 | ADP |
| 3 | 219 | 0.54 | 0.78 | 31 | ADP |
| 4 | 181 | 0.51 | 0.78 | 26 | ADP |
| 5 | 85 | 0.38 | 0.77 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 849 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 845 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 822 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2HVE · S120G mutant of human nucleoside diphosphate kinase A complexed with ADP · the same entry in another collection · chain C against C, TM-score 1.00
- P15531 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase a (P15531) · 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 P15531
- Elsewhere: RCSB PDB 2HVE · PDBe 2HVE · UniProt P15531
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.