Research workbench
Structure of porcine electron transfer flavoprotein-ubiquinone oxidoreductase in complexed with ubiquinone
Analyse Structure of porcine electron transfer flavoprotein-ubiquinone oxidoreductase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GMH
- Type
- protein
- Length
- 1,159 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Electron transfer flavoprotein-ubiquinone oxidoreductase
- EC
- 1.5.5.1
- UniProt
- P55931
- Ligands
- BHG, SF4, FAD, UQ5, NA
- Pockets
- 16 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Electron transfer flavoprotein-ubiquinone oxidoreductase (EC 1.5.5.1) | protein | 581 | 27% helix, 22% strand | P55931 |
| B | Electron transfer flavoprotein-ubiquinone oxidoreductase (EC 1.5.5.1) | protein | 578 | 25% helix, 19% strand | P55931 |
Ligands and binding sites
- BHG · hexyl beta-D-galactopyranoside · ligand · 3 copies · chains A, B
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- UQ5 · 2,3-dimethoxy-5-methyl-6-(3,11,15,19-tetramethyl-eicosa-2,6,10,14,18-pentaenyl)-[1,4]benzoquinone · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 780 | 0.89 | 0.92 | 103 | FAD, UQ5 |
| 2 | 399 | 0.86 | 0.95 | 60 | FAD |
| 3 | 358 | 0.78 | 0.87 | 45 | UQ5 |
| 4 | 952 | 0.73 | 0.76 | 75 | empty |
| 5 | 167 | 0.53 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 240 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2GMH · Structure of Porcine Electron Transfer Flavoprotein-Ubiqui Oxidoreductase in Complexed… · the same entry in another collection · chain A against A, TM-score 1.00
- P55931 · AlphaFold monomer V2.0 prediction for electron transfer flavoprotein- ubiquinone… · a predicted model of the same protein · 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 P55931
- Elsewhere: RCSB PDB 2GMH · PDBe 2GMH · UniProt P55931
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