MolNFT v1 · #108948 · protein
Crystal structure of saccharomyces cerevisiae omp synthase in complex with PRP(NH)P
4WN3 · Orotate phosphoribosyltransferase 1: “Crystal structure of saccharomyces cerevisiae omp synthase in complex with PRP(NH)P”. X-ray diffraction, 2 ligands (3R3, MG), 3 pockets (best druggability 0.53). MolNFT v1 #108948 on GenesisL1…
- PDB
- 4WN3
- Type
- protein
- Length
- 220 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotate phosphoribosyltransferase 1
- EC
- 2.4.2.10
- UniProt
- P13298
- Ligands
- 3R3, MG
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orotate phosphoribosyltransferase 1 (EC 2.4.2.10) | protein | 220 | 43% helix, 22% strand | P13298 |
Ligands and binding sites
- 3R3 · [[[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]oxy-oxidanyl-phosphoryl]amino]phosphonic acid · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.53 | 0.79 | 30 | empty |
| 2 | 62 | 0.32 | 0.75 | 12 | empty |
| 3 | 52 | 0.29 | 0.76 | 21 | MG, 3R3 |
Compared structures
- 4WN3 · Crystal structure of Saccharomyces cerevisiae OMP synthase in complex with PRP(NH)P · 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 0.96
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 4WN3 · PDBe 4WN3 · UniProt P13298
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