MolNFT v1 · #46964 · protein
High resolution crystal structures of vaccinia virus dutpase
2OKD · Deoxyuridine 5'-triphosphate nucleotidohydrolase: “High resolution crystal structures of vaccinia virus dutpase”. X-ray diffraction, 1 ligand (CL), 4 pockets (best druggability 0.76). MolNFT v1 #46964 on GenesisL1: 3D structure…
- PDB
- 2OKD
- Type
- protein
- Length
- 372 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
- CL
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 124 | 3% helix, 46% strand | — |
| B | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 123 | 3% helix, 46% strand | — |
| C | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 125 | 4% helix, 45% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.76 | 0.86 | 61 | EDO |
| 2 | 138 | 0.47 | 0.78 | 28 | empty |
| 3 | 94 | 0.41 | 0.78 | 21 | EDO |
| 4 | 72 | 0.36 | 0.77 | 18 | EDO |
Interfaces
3 interfaces between chains.
- A–C · 1515 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1448 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1445 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 2OKD · 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 2OKD · PDBe 2OKD
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