Research workbench
Correlation of X-ray deduced and experimental amino acid sequences of trimethylamine dehydrogenase
Analyse Correlation of X-ray deduced and experimental amino acid sequences of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2TMD
- 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
- 16 · best druggability 0.86
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
16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 389 | 0.86 | 0.95 | 47 | empty |
| 2 | 745 | 0.86 | 0.89 | 88 | empty |
| 3 | 154 | 0.82 | 0.97 | 30 | FMN |
| 4 | 153 | 0.81 | 0.97 | 30 | FMN |
| 5 | 135 | 0.74 | 0.93 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 6398 Ų buried · 91 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 2TMD · Correlation of X-ray deduced and experimental amino acid sequences 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 2TMD · PDBe 2TMD · UniProt P16099
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