Research workbench
Crystal structure of nucleoside diphosphate kinase in complex with ATP analog
Analyse Crystal structure of nucleoside diphosphate kinase in complex with ATP analog in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DXD
- Type
- protein
- Length
- 308 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- O58429
- Ligands
- ANP, CL
- Pockets
- 7 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 154 | 45% helix, 18% strand | O58429 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
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 | 189 | 0.51 | 0.77 | 23 | ANP |
| 2 | 176 | 0.50 | 0.77 | 26 | ANP |
| 3 | 112 | 0.36 | 0.74 | 15 | empty |
| 4 | 70 | 0.35 | 0.77 | 20 | empty |
| 5 | 60 | 0.29 | 0.74 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1105 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2DXD · Crystal structure of nucleoside diphosphate kinase in complex with ATP analog · the same entry in another collection · chain A against A, TM-score 1.00
- O58429 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase (O58429) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 O58429
- Elsewhere: RCSB PDB 2DXD · PDBe 2DXD · UniProt O58429
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