MolNFT v1 · #140106 · protein
Crystal structure of adenine phosphoribosyltransferase from yersinia pseudotuberculosis with prpp.
5Y07: “Crystal structure of adenine phosphoribosyltransferase from yersinia pseudotuberculosis with prpp.”. X-ray diffraction, 3 ligands (PRP, NA, MG), 3 pockets (best druggability 0.64). MolNFT v1 #140106 on GenesisL1: 3D structure…
- PDB
- 5Y07
- Type
- protein
- Length
- 357 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenine phosphoribosyltransferase
- EC
- 2.4.2.7
- UniProt
- Q66DQ2
- Ligands
- PRP, NA, MG
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenine phosphoribosyltransferase (EC 2.4.2.7) | protein | 179 | 35% helix, 32% strand | Q66DQ2 |
| B | Adenine phosphoribosyltransferase (EC 2.4.2.7) | protein | 178 | 36% helix, 34% strand | Q66DQ2 |
Ligands and binding sites
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
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 | 385 | 0.64 | 0.78 | 35 | PRP, MG |
| 2 | 442 | 0.63 | 0.77 | 42 | PRP, MG |
| 3 | 57 | 0.27 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1452 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5Y07 · Crystal structure of adenine phosphoribosyltransferase from Yersinia pseudotuberculosis… · the same entry in another collection · chain A against A, TM-score 1.00
- Q66DQ2 · AlphaFold monomer V2.0 prediction for adenine phosphoribosyltransferase (Q66DQ2) · a predicted model of the same protein · chain B 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 Q66DQ2
- Elsewhere: RCSB PDB 5Y07 · PDBe 5Y07 · UniProt Q66DQ2
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