Research workbench
Dithionite reduced dmso reductase from rhodobacter capsulatus
Analyse Dithionite reduced dmso reductase from rhodobacter capsulatus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DMR
- Type
- protein
- Length
- 771 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dmso reductase
- UniProt
- Q52675
- Ligands
- PGD, SO2, 4MO, O
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dmso reductase | protein | 771 | 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 · 2 copies · chains A
- SO2 · Sulfur dioxide · ligand · chains A
- 4MO · Molybdenum(iv) ion · metal · chains A
- O · Oxygen atom · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.84 | 0.95 | 52 | PGD, 4MO, O |
| 2 | 377 | 0.80 | 0.89 | 56 | PGD |
| 3 | 60 | 0.73 | 0.98 | 17 | empty |
| 4 | 216 | 0.53 | 0.77 | 34 | SO2 |
| 5 | 56 | 0.51 | 0.87 | 20 | empty |
Compared structures
- 2DMR · Dithionite reduced dmso reductase from rhodobacter capsulatus · 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 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 Q52675
- Elsewhere: RCSB PDB 2DMR · PDBe 2DMR · UniProt Q52675
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