Research workbench
Crystal structure of a nucleoside diphosphate kinase from campylobacter jejuni
Analyse Crystal structure of a nucleoside diphosphate kinase from campylobacter jejuni in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PJ9
- Type
- protein
- Length
- 549 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- Q9PIG7
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 137 | 45% helix, 19% strand | Q9PIG7 |
| C | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 136 | 43% helix, 21% strand | Q9PIG7 |
| D | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 139 | 47% helix, 17% strand | Q9PIG7 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.52 | 0.75 | 29 | SO4 |
| 2 | 265 | 0.50 | 0.74 | 39 | SO4 |
| 3 | 198 | 0.50 | 0.76 | 29 | SO4 |
| 4 | 151 | 0.47 | 0.77 | 23 | empty |
| 5 | 191 | 0.46 | 0.74 | 25 | SO4 |
Interfaces
4 interfaces between chains.
- B–C · 723 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 718 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 453 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 42 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3PJ9 · Crystal structure of a Nucleoside Diphosphate Kinase from Campylobacter jejuni · the same entry in another collection · chain A against A, TM-score 1.00
- Q9PIG7 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase (Q9PIG7) · a predicted model of the same protein · chain D 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 Q9PIG7
- Elsewhere: RCSB PDB 3PJ9 · PDBe 3PJ9 · UniProt Q9PIG7
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