Research workbench
Crystal structure of nucleoside diphosphate kinase from thermus thermophilus HB8 in complex with ATP and ADP
Analyse Crystal structure of nucleoside diphosphate kinase from thermus thermophilus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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