Research workbench
Structure of a halophilic nucleoside diphosphate kinase from halobacterium salinarum in complex with cdp
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
- 2AZ3
- Type
- protein
- Length
- 1,367 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- P61136
- Ligands
- CDP, MG
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F, G, H | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 152 | 41% helix, 16% strand | P61136 |
| B, I | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 151 | 40% helix, 16% strand | P61136 |
| C | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 153 | 42% helix, 16% strand | P61136 |
Ligands and binding sites
- CDP · Cytidine-5'-diphosphate · ligand · 9 copies · chains A, B, C, F, D, E, G, H, I
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.85 | 0.86 | 108 | empty |
| 2 | 212 | 0.73 | 0.89 | 29 | empty |
| 3 | 286 | 0.63 | 0.81 | 36 | MG, CDP |
| 4 | 522 | 0.63 | 0.76 | 67 | CDP |
| 5 | 305 | 0.58 | 0.77 | 32 | empty |
Interfaces
18 interfaces between chains.
- E–H · 1076 Ų buried · 22 hydrogen bonds · protein-protein
- F–G · 1053 Ų buried · 23 hydrogen bonds · protein-protein
- D–I · 1033 Ų buried · 18 hydrogen bonds · protein-protein
- H–I · 820 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 819 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2AZ3 · Structure of a halophilic nucleoside diphosphate kinase from Halobacterium salinarum in… · the same entry in another collection · chain I against I, TM-score 1.00
- P61136 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase (P61136) · a predicted model of the same protein · chain B 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 P61136
- Elsewhere: RCSB PDB 2AZ3 · PDBe 2AZ3 · UniProt P61136
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