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Crystal structure of monotopic membrane protein (S)-mandelate dehydrogenase
Analyse Crystal structure of monotopic membrane protein (S)-mandelate dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BFG
- Type
- protein
- Length
- 746 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Pseudomonas putida
- Molecule
- (S)-mandelate dehydrogenase
- EC
- 1.1.99.31
- UniProt
- P20932
- Ligands
- FMN, NA, SO4, PO4
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.2 · 1 distinct chain · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | (S)-mandelate dehydrogenase (EC 1.1.99.31) | protein | 373 | 50% helix, 13% strand | P20932 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
- SO4 · Sulfate ion · ion · chains A
- PO4 · Phosphate ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- CIT · Citric acid · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains B
- LMT · Dodecyl-beta-D-maltoside · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 809 | 0.82 | 0.85 | 72 | FMN, GOL, LMT |
| 2 | 772 | 0.81 | 0.84 | 70 | FMN, GOL |
| 3 | 99 | 0.54 | 0.84 | 20 | empty |
| 4 | 100 | 0.50 | 0.82 | 20 | empty |
| 5 | 145 | 0.45 | 0.76 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1479 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6BFG · Crystal structure of monotopic membrane protein (S)-mandelate dehydrogenase · the same entry in another collection · chain A against A, TM-score 1.00
- P20932 · AlphaFold monomer V2.0 prediction for (S)-mandelate dehydrogenase (P20932) · 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 P20932
- Elsewhere: RCSB PDB 6BFG · PDBe 6BFG · UniProt P20932
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