Research workbench
The crystal structure of rhodobacter sphaeroides dimethylsulfoxide reductase reveals two distinct molybdenum coordination environments.
Analyse The crystal structure of rhodobacter sphaeroides dimethylsulfoxide reductase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EU1
- Type
- protein
- Length
- 767 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dimethyl sulfoxide reductase
- EC
- 1.8.99.-
- UniProt
- Q57366
- Ligands
- MGD, GLC, CD, 6MO, O, SO4
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dimethyl sulfoxide reductase (EC 1.8.99.-) | protein | 767 | 33% helix, 18% strand | Q57366 |
Ligands and binding sites
- MGD · 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
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains A
- CD · Cadmium ion · metal · chains A
- 6MO · Molybdenum(vi) ion · metal · chains A
- O · Oxygen atom · ion · 2 copies · chains A
- SO4 · Sulfate ion · ion · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.84 | 0.95 | 50 | MGD, 6MO, O |
| 2 | 482 | 0.81 | 0.88 | 60 | MGD |
| 3 | 60 | 0.74 | 0.99 | 16 | empty |
| 4 | 106 | 0.57 | 0.85 | 20 | empty |
| 5 | 254 | 0.50 | 0.74 | 33 | EPE |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 1EU1 · The crystal structure of rhodobacter sphaeroides dimethylsulfoxide reductase reveals two… · the same entry in another collection · chain A against A, TM-score 1.00
- Q57366 · 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 Q57366
- Elsewhere: RCSB PDB 1EU1 · PDBe 1EU1 · UniProt Q57366
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