MolNFT v1 · #82965 · protein
Ternary complex of thermus thermophilus HB8 uridine-cytidine kinase with substrates
3W34 · Uridine kinase: “Ternary complex of thermus thermophilus HB8 uridine-cytidine kinase with substrates”. X-ray diffraction, 2 ligands (CTN, ACP), 4 pockets (best druggability 0.64). MolNFT v1 #82965 on GenesisL1: 3D structure, binding…
- PDB
- 3W34
- Type
- protein
- Length
- 411 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
- 4 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine kinase (EC 2.7.1.48) | protein | 208 | 50% helix, 22% strand | Q5SKR5 |
| B | Uridine kinase (EC 2.7.1.48) | protein | 203 | 49% helix, 19% 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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 327 | 0.64 | 0.80 | 61 | CTN, ACP |
| 2 | 190 | 0.63 | 0.84 | 33 | CTN, ACP |
| 3 | 105 | 0.38 | 0.75 | 20 | empty |
| 4 | 50 | 0.29 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 914 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3W34 · Ternary complex of Thermus thermophilus HB8 uridine-cytidine kinase with substrates · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SKR5 · AlphaFold monomer V2.0 prediction for uridine kinase (Q5SKR5) · a predicted model of the same protein · chain B 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 Q5SKR5
- Elsewhere: RCSB PDB 3W34 · PDBe 3W34 · UniProt Q5SKR5
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