Research workbench
Structural and biochemical characterization of recombinant wild type trimethylamine dehydrogenase from methylophilus methylotrophus (sp. W3A1)
Analyse Structural and biochemical characterization of recombinant wild type… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DJN
- 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
- 15 · best druggability 0.87
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
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 849 | 0.87 | 0.90 | 106 | empty |
| 2 | 382 | 0.86 | 0.95 | 48 | empty |
| 3 | 148 | 0.81 | 0.97 | 32 | FMN |
| 4 | 137 | 0.81 | 0.98 | 30 | FMN |
| 5 | 125 | 0.77 | 0.95 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 6400 Ų buried · 96 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 1DJN · Structural and biochemical characterization of recombinant wild type 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 1DJN · PDBe 1DJN · UniProt P16099
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