MolNFT v1 · #71350 · protein
Crystal structure of deoxyuridine 5-triphosphate nucleotidohydrolase from brucella melitensis, orthorhombic crystal form
3MBQ · Deoxyuridine 5'-triphosphate nucleotidohydrolase: “Crystal structure of deoxyuridine 5-triphosphate nucleotidohydrolase from brucella melitensis, orthorhombic…”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.60).…
- PDB
- 3MBQ
- Type
- protein
- Length
- 406 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
- UniProt
- Q2YRG4
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 135 | 7% helix, 46% strand | Q2YRG4 |
| B | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 132 | 8% helix, 48% strand | Q2YRG4 |
| C | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 139 | 7% helix, 44% strand | Q2YRG4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, C, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains A, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.60 | 0.89 | 23 | empty |
| 2 | 248 | 0.55 | 0.77 | 33 | EDO, GOL |
| 3 | 178 | 0.54 | 0.79 | 31 | EDO |
| 4 | 221 | 0.53 | 0.77 | 32 | EDO |
| 5 | 61 | 0.27 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1849 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1657 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1546 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 3MBQ · Crystal structure of deoxyuridine 5-triphosphate nucleotidohydrolase from Brucella… · the same entry in another collection · chain A against A, TM-score 1.00
- Q2YRG4 · AlphaFold monomer V2.0 prediction for deoxyuridine 5'-triphosphate nucleotidohydrolase… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q2YRG4
- Elsewhere: RCSB PDB 3MBQ · PDBe 3MBQ · UniProt Q2YRG4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.