Research workbench
3'-phosphorylated nucleotides binding to nucleoside diphosphate kinase
Analyse 3'-phosphorylated nucleotides binding to nucleoside diphosphate kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BUX
- Type
- protein
- Length
- 450 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- P22887
- Ligands
- PPS
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 150 | 43% helix, 17% strand | P22887 |
Ligands and binding sites
- PPS · 3'-phosphate-adenosine-5'-phosphate sulfate · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.63 | 0.80 | 31 | empty |
| 2 | 172 | 0.51 | 0.78 | 26 | PPS |
| 3 | 191 | 0.51 | 0.77 | 29 | PPS |
| 4 | 161 | 0.47 | 0.77 | 24 | PPS |
Interfaces
3 interfaces between chains.
- B–C · 766 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 765 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 760 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1BUX · 3'-phosphorylated nucleotides binding to nucleoside diphosphate kinase · the same entry in another collection · chain A against A, TM-score 1.00
- P22887 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase, cytosolic (P22887) · 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 P22887
- Elsewhere: RCSB PDB 1BUX · PDBe 1BUX · UniProt P22887
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