MolNFT v1 · #26289 · protein
Crystal structure of nucleoside diphosphate kinase from thermus thermophilus HB8 in complex with ATP and ADP
1WKL · Nucleotide diphosphate kinase: “Crystal structure of nucleoside diphosphate kinase from thermus thermophilus HB8 in complex with ATP and ADP”. X-ray diffraction, 4 ligands (PHS, ADP, ATP), 3 pockets (best druggability 0.50). MolNFT…
- PDB
- 1WKL
- Type
- protein
- Length
- 274 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleotide diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- Q5SLV5
- Ligands
- PHS, ADP, ATP, MG
- Pockets
- 3 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nucleotide diphosphate kinase (EC 2.7.4.6) | protein | 137 | 47% helix, 18% strand | Q5SLV5 |
Ligands and binding sites
- PHS · Phosphonic acid · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- ATP · Adenosine-5'-triphosphate · ligand · chains B
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.50 | 0.77 | 22 | PHS, ADP |
| 2 | 184 | 0.49 | 0.76 | 26 | MG, ATP |
| 3 | 124 | 0.44 | 0.76 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 728 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1WKL · Crystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8 in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SLV5 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase (Q5SLV5) · 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 Q5SLV5
- Elsewhere: RCSB PDB 1WKL · PDBe 1WKL · UniProt Q5SLV5
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