MolNFT v1 · #27989 · protein
Crystal structure of xanthine phosphoribosyltransferase from bacillus subtilis.
1Y0B: “Crystal structure of xanthine phosphoribosyltransferase from bacillus subtilis.”. X-ray diffraction, 2 ligands (G4P, NA), 4 pockets (best druggability 0.85). MolNFT v1 #27989 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1Y0B
- Type
- protein
- Length
- 768 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xanthine phosphoribosyltransferase
- EC
- 2.4.2.-
- UniProt
- P42085
- Ligands
- G4P, NA
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xanthine phosphoribosyltransferase (EC 2.4.2.-) | protein | 193 | 31% helix, 34% strand | P42085 |
| B | Xanthine phosphoribosyltransferase (EC 2.4.2.-) | protein | 192 | 32% helix, 32% strand | P42085 |
| C | Xanthine phosphoribosyltransferase (EC 2.4.2.-) | protein | 189 | 33% helix, 33% strand | P42085 |
| D | Xanthine phosphoribosyltransferase (EC 2.4.2.-) | protein | 194 | 32% helix, 32% strand | P42085 |
Ligands and binding sites
- G4P · Guanosine-5',3'-tetraphosphate · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.85 | 0.87 | 77 | NA, G4P |
| 2 | 1096 | 0.80 | 0.82 | 73 | NA, G4P |
| 3 | 88 | 0.57 | 0.87 | 20 | empty |
| 4 | 105 | 0.49 | 0.81 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1638 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1606 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 372 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 183 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 99 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1Y0B · Crystal Structure of Xanthine Phosphoribosyltransferase from Bacillus subtilis. · the same entry in another collection · chain D against D, TM-score 1.00
- P42085 · AlphaFold monomer V2.0 prediction for xanthine phosphoribosyltransferase (P42085) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P42085
- Elsewhere: RCSB PDB 1Y0B · PDBe 1Y0B · UniProt P42085
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