Research workbench
B. subtilis dutpase yncf in complex with du, ppi and mg (P212121)
Analyse B. subtilis dutpase yncf in complex with du, ppi and mg (P212121) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AOZ
- Type
- protein
- Length
- 413 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
- 5 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 43% 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, 45% strand | O31801 |
| B | Probable deoxyuridine 5'-triphosphate nucleotidohydrolase yncf (EC 3.6.1.23) | protein | 143 | 3% helix, 43% strand | O31801 |
| C | Probable deoxyuridine 5'-triphosphate nucleotidohydrolase yncf (EC 3.6.1.23) | protein | 140 | 4% 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 · chains B, C
- ACT · Acetate ion · additive · 2 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.77 | 0.95 | 31 | POP, MG, DUR |
| 2 | 186 | 0.77 | 0.92 | 37 | DUR, POP, MG |
| 3 | 186 | 0.50 | 0.76 | 30 | DUR, ACT |
| 4 | 143 | 0.42 | 0.74 | 25 | empty |
| 5 | 56 | 0.38 | 0.79 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2256 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 1939 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 1822 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 4AOZ · B. subtilis dUTPase YncF in complex with dU, PPi and Mg (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 0.99
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 4AOZ · PDBe 4AOZ · UniProt O31801
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