MolNFT v1 · #154874 · protein
Crystal structure of xanthine-guanine phosphoribosyltransferase (xgprt) from yersinia pestis in P21212 space group with sulphate ions in the active site
6KP5 · Xanthine phosphoribosyltransferase: “Crystal structure of xanthine-guanine phosphoribosyltransferase (xgprt) from yersinia pestis in P21212 space…”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.54). MolNFT v1…
- PDB
- 6KP5
- Type
- protein
- Length
- 277 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xanthine phosphoribosyltransferase
- EC
- 2.4.2.22
- UniProt
- Q8ZC05
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xanthine phosphoribosyltransferase (EC 2.4.2.22) | protein | 139 | 31% helix, 29% strand | Q8ZC05 |
| B | Xanthine phosphoribosyltransferase (EC 2.4.2.22) | protein | 138 | 31% helix, 26% strand | Q8ZC05 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.54 | 0.77 | 31 | SO4 |
| 2 | 150 | 0.45 | 0.76 | 32 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1504 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 6KP5 · crystal structure of Xanthine-guanine phosphoribosyltransferase (XGPRT) from Yersinia… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ZC05 · AlphaFold monomer V2.0 prediction for xanthine-guanine phosphoribosyltransferase (Q8ZC05) · 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 Q8ZC05
- Elsewhere: RCSB PDB 6KP5 · PDBe 6KP5 · UniProt Q8ZC05
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