Research workbench
Structural and biochemical characterization of recombinant C30A mutant of trimethylamine dehydrogenase from methylophilus methylotrophus (sp. W3A1)
Analyse Structural and biochemical characterization of recombinant C30A mutant of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DJQ
- Type
- protein
- Length
- 1,458 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trimethylamine dehydrogenase
- EC
- 1.5.99.7
- UniProt
- P16099
- Ligands
- SF4, FMN, ADP
- Pockets
- 14 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 17% 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 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.88 | 0.90 | 108 | empty |
| 2 | 382 | 0.86 | 0.95 | 45 | empty |
| 3 | 153 | 0.82 | 0.98 | 31 | FMN |
| 4 | 155 | 0.81 | 0.97 | 32 | FMN |
| 5 | 360 | 0.73 | 0.85 | 56 | ADP |
Interfaces
1 interface between chains.
- A–B · 6456 Ų buried · 95 hydrogen bonds · protein-protein
Compared structures
- 1DJQ · Structural and biochemical characterization of recombinant C30A mutant of trimethylamine… · the same entry in another collection · chain A against A, 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
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
- Elsewhere: RCSB PDB 1DJQ · PDBe 1DJQ · UniProt P16099
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