MolNFT v1 · #13594 · protein
Crystal structure of salmonella typhimurium omp synthase in complex with mgprpp and orotate
1LH0: “Crystal structure of salmonella typhimurium omp synthase in complex with mgprpp and orotate”. X-ray diffraction, 3 ligands (ORO, PRP, MG), 3 pockets (best druggability 0.76). MolNFT v1 #13594 on GenesisL1: 3D structure, binding…
- PDB
- 1LH0
- Type
- protein
- Length
- 419 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Omp synthase
- EC
- 2.4.2.10
- UniProt
- P08870
- Ligands
- ORO, PRP, MG
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Omp synthase (EC 2.4.2.10) | protein | 213 | 45% helix, 24% strand | P08870 |
| B | Omp synthase (EC 2.4.2.10) | protein | 206 | 45% helix, 27% strand | P08870 |
Ligands and binding sites
- ORO · Orotic acid · ligand · 2 copies · chains A, B
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · chains A, B
- MG · Magnesium ion · metal · chains 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 | 238 | 0.76 | 0.90 | 36 | MG, ORO, PRP |
| 2 | 154 | 0.58 | 0.83 | 24 | ORO |
| 3 | 139 | 0.42 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1563 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 1LH0 · Crystal Structure of Salmonella typhimurium OMP Synthase in Complex with MGPRPP and… · the same entry in another collection · chain A against A, TM-score 1.00
- P08870 · AlphaFold monomer V2.0 prediction for orotate phosphoribosyltransferase (P08870) · a predicted model of the same protein · chain A 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 P08870
- Elsewhere: RCSB PDB 1LH0 · PDBe 1LH0 · UniProt P08870
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