MolNFT v1 · #167980 · protein
Re-interpretation of ppgpp (G4P) electron density in the deposited crystal structure of xanthine phosphoribosyltransferase (xprt) (1Y0B).
6W1I: “Re-interpretation of ppgpp (G4P) electron density in the deposited crystal structure of xanthine…”. X-ray diffraction, 2 ligands (G4P, NA), 3 pockets (best druggability 0.86). MolNFT v1 #167980 on GenesisL1: 3D structure, binding…
- PDB
- 6W1I
- Type
- protein
- Length
- 773 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xanthine phosphoribosyltransferase
- EC
- 2.4.2.22
- UniProt
- P42085
- Ligands
- G4P, NA
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xanthine phosphoribosyltransferase (EC 2.4.2.22) | protein | 193 | 32% helix, 34% strand | P42085 |
| B | Xanthine phosphoribosyltransferase (EC 2.4.2.22) | protein | 194 | 32% helix, 32% strand | P42085 |
| C | Xanthine phosphoribosyltransferase (EC 2.4.2.22) | protein | 192 | 33% helix, 33% strand | P42085 |
| D | Xanthine phosphoribosyltransferase (EC 2.4.2.22) | protein | 194 | 32% helix, 33% 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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1008 | 0.86 | 0.87 | 96 | NA, G4P |
| 2 | 1143 | 0.81 | 0.82 | 74 | NA, G4P |
| 3 | 88 | 0.50 | 0.83 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1616 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1606 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 374 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 178 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 134 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 6W1I · Re-interpretation of ppGpp (G4P) electron density in the deposited crystal structure of… · 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 6W1I · PDBe 6W1I · UniProt P42085
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