Research workbench
Azt diphosphate binding to nucleoside diphosphate kinase
Analyse Azt diphosphate 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
- 1LWX
- 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
- AZD, MG
- Pockets
- 5 · best druggability 0.65
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
- AZD · 3'-azido-3'-deoxythymidine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.65 | 0.79 | 39 | empty |
| 2 | 171 | 0.54 | 0.80 | 25 | MG, AZD |
| 3 | 157 | 0.53 | 0.80 | 25 | AZD |
| 4 | 160 | 0.51 | 0.79 | 24 | MG, AZD |
| 5 | 56 | 0.26 | 0.73 | 28 | empty |
Interfaces
3 interfaces between chains.
- B–C · 780 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 777 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 772 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1LWX · Azt diphosphate 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 0.98
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 P22887
- Elsewhere: RCSB PDB 1LWX · PDBe 1LWX · UniProt P22887
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