MolNFT v1 · #22997 · protein
Trimethylamine N-oxide reductase from shewanella massilia
1TMO: “Trimethylamine N-oxide reductase from shewanella massilia”. X-ray diffraction, 2 ligands (2MD, 2MO), 5 pockets (best druggability 0.88). MolNFT v1 #22997 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1TMO
- Type
- protein
- Length
- 794 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trimethylamine N-oxide reductase
- EC
- 1.6.6.9
- UniProt
- O87948
- Ligands
- 2MD, 2MO
- Pockets
- 5 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trimethylamine N-oxide reductase (EC 1.6.6.9) | protein | 794 | 32% helix, 18% strand | O87948 |
Ligands and binding sites
- 2MD · Guanylate-O'-phosphoric acid mono-(2-amino-5,6-dimercapto-4-oxo-3,5,6,7,8A,9,10,10A-octahydro-4H-8-oxa-1,3,9,10-tetraaza-anthracen-7-ylmethyl) ester · ligand · 2 copies · chains A
- 2MO · Molybdenum (iv)oxide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1065 | 0.88 | 0.89 | 106 | 2MD, 2MO |
| 2 | 133 | 0.49 | 0.79 | 19 | empty |
| 3 | 107 | 0.45 | 0.79 | 23 | empty |
| 4 | 61 | 0.30 | 0.75 | 15 | empty |
| 5 | 62 | 0.27 | 0.73 | 12 | empty |
Compared structures
- 1TMO · Trimethylamine N-oxide reductase from shewanella massilia · the same entry in another collection · chain A against A, TM-score 1.00
- O87948 · AlphaFold monomer V2.0 prediction for trimethylamine-N-oxide reductase (O87948) · a predicted model of the same protein · chain A 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 O87948
- Elsewhere: RCSB PDB 1TMO · PDBe 1TMO · UniProt O87948
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