MolNFT v1 · #46962 · protein
High resolution crystal structures of vaccinia virus dutpase
2OKB · Deoxyuridine 5'-triphosphate nucleotidohydrolase: “High resolution crystal structures of vaccinia virus dutpase”. X-ray diffraction, 2 ligands (SO4, CL), 5 pockets (best druggability 0.80). MolNFT v1 #46962 on GenesisL1: 3D…
- PDB
- 2OKB
- Type
- protein
- Length
- 339 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyuridine 5'-triphosphate nucleotidohydrolase
- EC
- 3.6.1.23
- Ligands
- SO4, CL
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 113 | 4% helix, 50% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 2 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.80 | 0.88 | 65 | CL, EDO |
| 2 | 151 | 0.53 | 0.80 | 30 | SO4, EDO |
| 3 | 167 | 0.51 | 0.78 | 25 | SO4 |
| 4 | 156 | 0.51 | 0.79 | 25 | SO4 |
| 5 | 93 | 0.46 | 0.80 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 993 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 961 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 930 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2OKB · High Resolution Crystal Structures of Vaccinia Virus dUTPase · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 2OKB · PDBe 2OKB
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