Research workbench
Ternary complex between trimethylamine dehydrogenase and electron transferring flavoprotein
Analyse Ternary complex between trimethylamine dehydrogenase and electron transferring… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1O95
- Type
- protein
- Length
- 2,305 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trimethylamine dehydrogenase; Electron transfer flavoprotein beta-subunit; Electron…
- EC
- 1.5.99.7
- UniProt
- P16099, P53570, P53571
- Ligands
- FMN, ADP, SF4, AMP
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Trimethylamine dehydrogenase (EC 1.5.99.7) | protein | 729 | 33% helix, 17% strand | P16099 |
| C | Electron transfer flavoprotein beta-subunit | protein | 233 | 29% helix, 31% strand | P53570 |
| D, F | Electron transfer flavoprotein alpha-subunit | protein | 189 | 24% helix, 38% strand | P53571 |
| E | Electron transfer flavoprotein beta-subunit | protein | 236 | 31% helix, 31% strand | P53570 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- AMP · Adenosine monophosphate · ligand · 2 copies · chains C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.89 | 0.91 | 137 | empty |
| 2 | 336 | 0.85 | 0.95 | 50 | empty |
| 3 | 174 | 0.82 | 0.97 | 34 | FMN |
| 4 | 146 | 0.82 | 0.98 | 29 | FMN |
| 5 | 568 | 0.79 | 0.85 | 61 | AMP |
Interfaces
5 interfaces between chains.
- A–B · 6350 Ų buried · 96 hydrogen bonds · protein-protein
- C–D · 2281 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 2261 Ų buried · 41 hydrogen bonds · protein-protein
- A–E · 550 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 501 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 1O95 · Ternary complex between trimethylamine dehydrogenase and electron transferring… · the same entry in another collection · chain F against F, TM-score 1.00
- P16099 · AlphaFold monomer V2.0 prediction for trimethylamine dehydrogenase (P16099) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P53571 · AlphaFold monomer V2.0 prediction for electron transfer flavoprotein subunit alpha… · a predicted model of the same protein · chain D against A, TM-score 0.99
- P53570 · AlphaFold monomer V2.0 prediction for electron transfer flavoprotein subunit beta (P53570) · a predicted model of the same protein · chain E 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 P16099
- Every structure of UniProt P53570
- Every structure of UniProt P53571
- Elsewhere: RCSB PDB 1O95 · PDBe 1O95 · UniProt P16099 · UniProt P53570 · UniProt P53571
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