MolNFT v1 · #58095 · protein
Cmp-complex structure of uridine kinase from thermus thermophilus HB8
3ASZ: “Cmp-complex structure of uridine kinase from thermus thermophilus HB8”. X-ray diffraction, 1 ligand (C5P), 4 pockets (best druggability 0.70). MolNFT v1 #58095 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3ASZ
- 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
- C5P
- Pockets
- 4 · best druggability 0.70
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 | 203 | 49% helix, 19% strand | Q5SKR5 |
| B | Uridine kinase (EC 2.7.1.48) | protein | 208 | 50% helix, 22% strand | Q5SKR5 |
Ligands and binding sites
- C5P · Cytidine-5'-monophosphate · 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 | 75 | 0.70 | 0.95 | 20 | C5P |
| 2 | 240 | 0.60 | 0.80 | 41 | C5P |
| 3 | 216 | 0.49 | 0.75 | 35 | empty |
| 4 | 50 | 0.26 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 855 Ų buried · 12 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 3ASZ · PDBe 3ASZ · UniProt Q5SKR5
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