MolNFT v1 · #15990 · protein
Crystal structure of myxococcus xanthus nucleoside diphosphate kinase and its interaction with a nucleotide substrate at 2.0 ångströms resolution
1NLK: “Crystal structure of myxococcus xanthus nucleoside diphosphate kinase and its interaction with a nucleotide…”. X-ray diffraction, 2 ligands (ADP, MG), 2 pockets (best druggability 0.53). MolNFT v1 #15990 on GenesisL1: 3D structure…
- PDB
- 1NLK
- Type
- protein
- Length
- 286 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
- P15266
- Ligands
- ADP, MG
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R, L | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 143 | 45% helix, 20% strand | P15266 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains R, L
- MG · Magnesium ion · metal · 2 copies · chains R, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 205 | 0.53 | 0.77 | 29 | MG, ADP |
| 2 | 194 | 0.50 | 0.76 | 27 | MG, ADP |
Interfaces
1 interface between chains.
- R–L · 1092 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1NLK · Crystal structure of myxococcus xanthus nucleoside diphosphate kinase and its interaction… · the same entry in another collection · chain R against R, TM-score 1.00
- P15266 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase (P15266) · a predicted model of the same protein · chain R 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 P15266
- Elsewhere: RCSB PDB 1NLK · PDBe 1NLK · UniProt P15266
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