Research workbench
Crystal structure of nucleotide diphosphate kinase from pyrococcus horikoshii
Analyse Crystal structure of nucleotide diphosphate kinase from pyrococcus horikoshii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CWK
- Type
- protein
- Length
- 305 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside-diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- O58429
- Pockets
- 6 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoside-diphosphate kinase (EC 2.7.4.6) | protein | 153 | 45% helix, 18% strand | O58429 |
| B | Nucleoside-diphosphate kinase (EC 2.7.4.6) | protein | 152 | 45% helix, 18% strand | O58429 |
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.49 | 0.76 | 25 | empty |
| 2 | 169 | 0.48 | 0.76 | 24 | empty |
| 3 | 90 | 0.38 | 0.76 | 22 | empty |
| 4 | 110 | 0.35 | 0.73 | 15 | empty |
| 5 | 86 | 0.35 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1072 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 2CWK · Crystal structure of nucleotide diphosphate kinase from Pyrococcus horikoshii · the same entry in another collection · chain A against A, TM-score 1.00
- O58429 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase (O58429) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 O58429
- Elsewhere: RCSB PDB 2CWK · PDBe 2CWK · UniProt O58429
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