Research workbench
Crystal structure of saccharomyces cerevisiae omp synthase in complex with PRP(CH2)P
Analyse Crystal structure of saccharomyces cerevisiae omp synthase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WML
- Type
- protein
- Length
- 216 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
- PPC, MG
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orotate phosphoribosyltransferase 1 (EC 2.4.2.10) | protein | 216 | 44% helix, 23% strand | P13298 |
Ligands and binding sites
- PPC · 1-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-5-O-phosphono-alpha-D-ribofuranose · 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
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 | 213 | 0.53 | 0.77 | 25 | empty |
| 2 | 87 | 0.38 | 0.76 | 15 | empty |
Compared structures
- 4WML · Crystal structure of Saccharomyces cerevisiae OMP synthase in complex with PRP(CH2)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 4WML · PDBe 4WML · UniProt P13298
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.