Research workbench
Structure of a halophilic nucleoside diphosphate kinase from halobacterium salinarum
Analyse Structure of a halophilic nucleoside diphosphate kinase from halobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AZ1
- Type
- protein
- Length
- 921 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
- P61136
- Ligands
- CA
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 155 | 46% helix, 15% strand | P61136 |
| B | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 151 | 38% helix, 16% strand | P61136 |
| E | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 154 | 44% helix, 16% strand | P61136 |
| F | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 151 | 41% helix, 16% strand | P61136 |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 819 | 0.82 | 0.84 | 76 | empty |
| 2 | 249 | 0.75 | 0.89 | 30 | empty |
| 3 | 227 | 0.73 | 0.88 | 29 | empty |
| 4 | 186 | 0.49 | 0.77 | 29 | empty |
| 5 | 139 | 0.49 | 0.79 | 24 | CA |
Interfaces
12 interfaces between chains.
- A–D · 1087 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 1075 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 1046 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 827 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 824 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2AZ1 · Structure of a halophilic nucleoside diphosphate kinase from Halobacterium salinarum · the same entry in another collection · chain E against E, TM-score 1.00
- P61136 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase (P61136) · a predicted model of the same protein · chain F 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 P61136
- Elsewhere: RCSB PDB 2AZ1 · PDBe 2AZ1 · UniProt P61136
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