Research workbench
Nucleoside diphosphate kinase isoform a from bovine retina
Analyse Nucleoside diphosphate kinase isoform a from bovine retina in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BHN
- Type
- protein
- Length
- 906 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate transferase
- EC
- 2.7.4.6
- UniProt
- P52174
- Ligands
- 35G, GDP
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Nucleoside diphosphate transferase (EC 2.7.4.6) | protein | 151 | 44% helix, 17% strand | P52174 |
Ligands and binding sites
- 35G · Guanosine-3',5'-monophosphate · ligand · 6 copies · chains A, B, C, D, E, F
- GDP · Guanosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 459 | 0.85 | 0.92 | 52 | empty |
| 2 | 478 | 0.85 | 0.92 | 51 | empty |
| 3 | 448 | 0.84 | 0.91 | 58 | empty |
| 4 | 454 | 0.83 | 0.90 | 80 | empty |
| 5 | 226 | 0.51 | 0.76 | 26 | 35G, GDP |
Interfaces
12 interfaces between chains.
- A–E · 1088 Ų buried · 17 hydrogen bonds · protein-protein
- C–F · 1069 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1043 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 827 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 822 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1BHN · Nucleoside diphosphate kinase isoform a from bovine retina · the same entry in another collection · chain B against B, TM-score 1.00
- P52174 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase a 1 (P52174) · a predicted model of the same protein · chain A 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 P52174
- Elsewhere: RCSB PDB 1BHN · PDBe 1BHN · UniProt P52174
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