MolNFT v1 · #8603 · protein
Dmso reductase modified by the presence of dms and air
1H5N · Dimethyl SULFOXIDE/TRIMETHYLAMINE N-oxide reductase: “Dmso reductase modified by the presence of dms and air”. X-ray diffraction, 3 ligands (PGD, 6MO, SO4), 13 pockets (best druggability 0.87). MolNFT v1 #8603 on GenesisL1: 3D…
- PDB
- 1H5N
- Type
- protein
- Length
- 1,531 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dimethyl SULFOXIDE/TRIMETHYLAMINE N-oxide reductase
- EC
- 1.7.2.3, 1.8.5.3
- UniProt
- Q52675
- Ligands
- PGD, 6MO, SO4
- Pockets
- 13 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dimethyl SULFOXIDE/TRIMETHYLAMINE N-oxide reductase (EC 1.7.2.3, 1.8.5.3) | protein | 765 | 34% helix, 18% strand | Q52675 |
| C | Dimethyl SULFOXIDE/TRIMETHYLAMINE N-oxide reductase (EC 1.7.2.3, 1.8.5.3) | protein | 766 | 34% helix, 18% strand | Q52675 |
Ligands and binding sites
- PGD · 2-amino-5,6-dimercapto-7-methyl-3,7,8A,9-tetrahydro-8-oxa-1,3,9,10-tetraaza-anthracen-4-one guanosine dinucleotide · ligand · 4 copies · chains A, C
- 6MO · Molybdenum(vi) ion · metal · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 604 | 0.87 | 0.92 | 98 | PGD, 6MO |
| 2 | 658 | 0.86 | 0.90 | 97 | PGD, 6MO |
| 3 | 54 | 0.73 | 0.99 | 15 | empty |
| 4 | 55 | 0.72 | 0.99 | 16 | empty |
| 5 | 223 | 0.50 | 0.75 | 29 | SO4 |
Interfaces
1 interface between chains.
- A–C · 137 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1H5N · Dmso reductase modified by the presence of dms and air · the same entry in another collection · chain A against A, TM-score 1.00
- Q52675 · AlphaFold monomer V2.0 prediction for dimethyl SULFOXIDE/TRIMETHYLAMINE N-oxide reductase… · 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 Q52675
- Elsewhere: RCSB PDB 1H5N · PDBe 1H5N · UniProt Q52675
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