Research workbench
Mutant structure of thermus thermophilus HB8 uridine-cytidine kinase
Analyse Mutant structure of thermus thermophilus HB8 uridine-cytidine kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W8R
- Type
- protein
- Length
- 413 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine kinase
- EC
- 2.7.1.48
- UniProt
- Q5SKR5
- Ligands
- CTN, ACP
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine kinase (EC 2.7.1.48) | protein | 207 | 49% helix, 22% strand | Q5SKR5 |
| B | Uridine kinase (EC 2.7.1.48) | protein | 206 | 48% helix, 22% strand | Q5SKR5 |
Ligands and binding sites
- CTN · 4-amino-1-beta-D-ribofuranosyl-2(1H)-pyrimidinone · ligand · 2 copies · chains A, B
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.63 | 0.80 | 46 | CTN, ACP |
| 2 | 233 | 0.63 | 0.82 | 40 | CTN, ACP |
| 3 | 231 | 0.50 | 0.75 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 893 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
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 Q5SKR5
- Elsewhere: RCSB PDB 3W8R · PDBe 3W8R · UniProt Q5SKR5
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