Research workbench
The crystal structure of a human nucleoside diphosphate kinase, NM23-H2
Analyse The crystal structure of a human nucleoside diphosphate kinase, NM23-H2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NSK
- Type
- protein
- Length
- 906 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
- P22392
- Pockets
- 13 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R, L, T, U, N, O | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 151 | 46% helix, 15% strand | P22392 |
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.88 | 0.89 | 117 | empty |
| 2 | 445 | 0.84 | 0.91 | 48 | empty |
| 3 | 451 | 0.84 | 0.91 | 52 | empty |
| 4 | 358 | 0.57 | 0.75 | 61 | empty |
| 5 | 217 | 0.49 | 0.75 | 28 | empty |
Interfaces
12 interfaces between chains.
- R–L · 1062 Ų buried · 17 hydrogen bonds · protein-protein
- U–N · 1062 Ų buried · 17 hydrogen bonds · protein-protein
- T–O · 1056 Ų buried · 16 hydrogen bonds · protein-protein
- L–N · 733 Ų buried · 9 hydrogen bonds · protein-protein
- R–T · 732 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1NSK · The crystal structure of a human nucleoside diphosphate kinase, NM23-H2 · the same entry in another collection · chain T against T, TM-score 1.00
- P22392 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase B (P22392) · a predicted model of the same protein · chain R against A, TM-score 0.98
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 P22392
- Elsewhere: RCSB PDB 1NSK · PDBe 1NSK · UniProt P22392
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