MolNFT v1 · #48398 · protein
S. cerevisiae orotate phosphoribosyltransferase complexed with orotic acid and prpp
2PS1 · Orotate phosphoribosyltransferase 1: “S. cerevisiae orotate phosphoribosyltransferase complexed with orotic acid and prpp”. X-ray diffraction, 3 ligands (ORO, PRP, MG), 2 pockets (best druggability 0.75). MolNFT v1 #48398 on…
- PDB
- 2PS1
- Type
- protein
- Length
- 448 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotate phosphoribosyltransferase 1
- EC
- 2.4.2.10
- UniProt
- P13298
- Ligands
- ORO, PRP, MG
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Orotate phosphoribosyltransferase 1 (EC 2.4.2.10) | protein | 224 | 41% helix, 28% strand | P13298 |
Ligands and binding sites
- ORO · Orotic acid · ligand · 2 copies · chains A, B
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · 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
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 320 | 0.75 | 0.87 | 38 | MG, ORO, PRP |
| 2 | 309 | 0.74 | 0.86 | 36 | MG, ORO, PRP |
Interfaces
1 interface between chains.
- A–B · 1601 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2PS1 · S. cerevisiae orotate phosphoribosyltransferase complexed with orotic acid and PRPP · the same entry in another collection · chain A against A, TM-score 1.00
- P13298 · AlphaFold monomer V2.0 prediction for orotate phosphoribosyltransferase 1 (P13298) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 P13298
- Elsewhere: RCSB PDB 2PS1 · PDBe 2PS1 · UniProt P13298
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