Research workbench
High resolution crystal structures of vaccinia virus dutpase
Analyse High resolution crystal structures of vaccinia virus dutpase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OL0
- Type
- protein
- Length
- 373 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
- DUD, MG, CL
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 124 | 4% helix, 46% strand | — |
| C | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 125 | 4% helix, 45% strand | — |
Ligands and binding sites
- DUD · Deoxyuridine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · chains B
- CL · Chloride ion · ion · chains A, B, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, C, A
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 | 376 | 0.75 | 0.86 | 60 | empty |
| 2 | 153 | 0.48 | 0.78 | 27 | MG, EDO, DUD |
| 3 | 101 | 0.46 | 0.79 | 21 | DUD |
| 4 | 99 | 0.41 | 0.77 | 22 | DUD |
Interfaces
3 interfaces between chains.
- A–B · 1511 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1453 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1452 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 2OL0 · 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 2OL0 · PDBe 2OL0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.