MolNFT v1 · #35020 · protein
Crystal structure of complex between adenine nucleotide and nucleoside diphosphate kinase
2DYA: “Crystal structure of complex between adenine nucleotide and nucleoside diphosphate kinase”. X-ray diffraction, 3 ligands (ADP, MG, CL), 6 pockets (best druggability 0.48). MolNFT v1 #35020 on GenesisL1: 3D structure, binding sites…
- PDB
- 2DYA
- Type
- protein
- Length
- 309 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
- ADP, MG, CL
- Pockets
- 6 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 154 | 45% helix, 18% strand | O58429 |
| B | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 155 | 44% helix, 18% strand | O58429 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.48 | 0.79 | 20 | MG, ADP |
| 2 | 125 | 0.46 | 0.78 | 19 | MG, ADP |
| 3 | 117 | 0.35 | 0.72 | 20 | CL |
| 4 | 77 | 0.33 | 0.75 | 24 | empty |
| 5 | 93 | 0.32 | 0.72 | 18 | CL |
Interfaces
1 interface between chains.
- A–B · 1113 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 2DYA · Crystal structure of complex between Adenine nucleotide and nucleoside diphosphate kinase · 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 2DYA · PDBe 2DYA · UniProt O58429
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