Research workbench
Crystal structure of human nucleoside diphosphate kinase a
Analyse Crystal structure of human nucleoside diphosphate kinase a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JXV
- Type
- protein
- Length
- 894 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase a
- EC
- 2.7.4.6
- UniProt
- P15531
- Pockets
- 14 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Nucleoside diphosphate kinase a (EC 2.7.4.6) | protein | 149 | 47% helix, 17% strand | P15531 |
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.88 | 0.89 | 105 | empty |
| 2 | 480 | 0.84 | 0.91 | 54 | empty |
| 3 | 441 | 0.84 | 0.91 | 49 | empty |
| 4 | 215 | 0.51 | 0.76 | 31 | empty |
| 5 | 221 | 0.50 | 0.75 | 34 | empty |
Interfaces
12 interfaces between chains.
- B–F · 1038 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 1034 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1027 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 824 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 821 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1JXV · Crystal Structure of Human Nucleoside Diphosphate Kinase A · 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 1JXV · PDBe 1JXV · UniProt P15531
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