Research workbench
Nucleoside diphosphate kinase isoform B from bovine retina
Analyse Nucleoside diphosphate kinase isoform B 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
- 1BE4
- Type
- protein
- Length
- 453 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate transferase
- EC
- 2.7.4.6
- UniProt
- P52175
- Ligands
- PCG
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Nucleoside diphosphate transferase (EC 2.7.4.6) | protein | 151 | 47% helix, 19% strand | P52175 |
Ligands and binding sites
- PCG · Cyclic guanosine monophosphate · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.68 | 0.82 | 45 | empty |
| 2 | 180 | 0.50 | 0.77 | 31 | PCG |
| 3 | 196 | 0.49 | 0.76 | 27 | PCG |
| 4 | 165 | 0.47 | 0.77 | 36 | empty |
| 5 | 151 | 0.45 | 0.76 | 25 | PCG |
Interfaces
3 interfaces between chains.
- A–C · 821 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 819 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 802 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1BE4 · Nucleoside diphosphate kinase isoform B from bovine retina · the same entry in another collection · chain A against A, TM-score 1.00
- P52175 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase a 2 (P52175) · 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 P52175
- Elsewhere: RCSB PDB 1BE4 · PDBe 1BE4 · UniProt P52175
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.