Research workbench
Crystal structure of putative mandelate racemase from bordetella bronchiseptica RB50 complexed with 2-OXOGLUTARATE/PHOSPHATE
Analyse Crystal structure of putative mandelate racemase from bordetella bronchiseptica… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OP2
- Type
- protein
- Length
- 743 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative mandelate racemase
- UniProt
- Q7WEE8
- Ligands
- AKG, MG, PO4
- Pockets
- 3 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative mandelate racemase | protein | 375 | 39% helix, 18% strand | Q7WEE8 |
| B | Putative mandelate racemase | protein | 368 | 40% helix, 18% strand | Q7WEE8 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 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 | 1095 | 0.88 | 0.89 | 105 | AKG |
| 2 | 127 | 0.66 | 0.89 | 24 | PO4 |
| 3 | 76 | 0.39 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1027 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3OP2 · Crystal structure of putative mandelate racemase from Bordetella bronchiseptica RB50… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q7WEE8
- Elsewhere: RCSB PDB 3OP2 · PDBe 3OP2 · UniProt Q7WEE8
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