MolNFT v1 · #86242 · protein
B. subtilis dutpase yncf in complex with du, ppi and mg B (P212121)
4B0H · Probable deoxyuridine 5'-triphosphate nucleotidohydrolase…: “B. subtilis dutpase yncf in complex with du, ppi and mg B (P212121)”. X-ray diffraction, 4 ligands (DUR, POP, MG), 4 pockets (best druggability 0.77). MolNFT v1 #86242 on…
- PDB
- 4B0H
- Type
- protein
- Length
- 416 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable deoxyuridine 5'-triphosphate nucleotidohydrolase yncf
- EC
- 3.6.1.23
- UniProt
- O31801
- Ligands
- DUR, POP, MG, CL
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable deoxyuridine 5'-triphosphate nucleotidohydrolase yncf (EC 3.6.1.23) | protein | 130 | 4% helix, 46% strand | O31801 |
| B, C | Probable deoxyuridine 5'-triphosphate nucleotidohydrolase yncf (EC 3.6.1.23) | protein | 143 | 3% helix, 42% strand | O31801 |
Ligands and binding sites
- DUR · 2'-deoxyuridine · ligand · 3 copies · chains A, B, C
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B, C
- MG · Magnesium ion · metal · 2 copies · chains A, B, C
- CL · Chloride ion · ion · 2 copies · chains A, C, B
- PG4 · Tetraethylene glycol · additive · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.77 | 0.92 | 39 | DUR, POP, MG |
| 2 | 150 | 0.75 | 0.93 | 36 | POP, MG, DUR |
| 3 | 182 | 0.49 | 0.76 | 30 | DUR |
| 4 | 138 | 0.42 | 0.75 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2274 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 1960 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 1842 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 4B0H · B. subtilis dUTPase YncF in complex with dU, PPi and Mg b (P212121) · the same entry in another collection · chain A against A, TM-score 1.00
- O31801 · AlphaFold monomer V2.0 prediction for probable deoxyuridine 5'-triphosphate… · a predicted model of the same protein · chain A 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 O31801
- Elsewhere: RCSB PDB 4B0H · PDBe 4B0H · UniProt O31801
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