MolNFT v1 · #46965 · protein
High resolution crystal structures of vaccinia virus dutpase
2OKE · Deoxyuridine 5'-triphosphate nucleotidohydrolase: “High resolution crystal structures of vaccinia virus dutpase”. X-ray diffraction, 3 ligands (DUP, MG, CL), 5 pockets (best druggability 0.83). MolNFT v1 #46965 on GenesisL1: 3D…
- PDB
- 2OKE
- Type
- protein
- Length
- 369 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
- DUP, MG, CL
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 123 | 5% helix, 45% strand | — |
Ligands and binding sites
- DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · 3 copies · chains A, C, B
- MG · Magnesium ion · metal · chains B, C
- CL · Chloride ion · ion · chains A, B, C
- EDO · 1,2-ethanediol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.83 | 0.95 | 40 | empty |
| 2 | 157 | 0.50 | 0.78 | 31 | DUP |
| 3 | 145 | 0.49 | 0.78 | 26 | DUP |
| 4 | 153 | 0.47 | 0.77 | 32 | MG, DUP |
| 5 | 124 | 0.37 | 0.74 | 36 | EDO |
Interfaces
3 interfaces between chains.
- A–C · 1507 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1492 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1450 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 2OKE · 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 2OKE · PDBe 2OKE
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