Research workbench
The "rhodanese" fold and catalytic mechanism of 3-mercaptopyruvate sulfotransferases: crystal structure of ssea from escherichia COLI
Analyse The "rhodanese" fold and catalytic mechanism of 3-mercaptopyruvate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1URH
- Type
- protein
- Length
- 518 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-mercaptopyruvate sulfurtransferase
- EC
- 2.8.1.2
- UniProt
- P31142
- Ligands
- SO3
- Pockets
- 8 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-mercaptopyruvate sulfurtransferase (EC 2.8.1.2) | protein | 262 | 32% helix, 14% strand | P31142 |
| B | 3-mercaptopyruvate sulfurtransferase (EC 2.8.1.2) | protein | 256 | 34% helix, 16% strand | P31142 |
Ligands and binding sites
- SO3 · Sulfite ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.60 | 0.77 | 57 | empty |
| 2 | 141 | 0.56 | 0.82 | 28 | empty |
| 3 | 167 | 0.54 | 0.80 | 20 | empty |
| 4 | 167 | 0.50 | 0.78 | 24 | empty |
| 5 | 122 | 0.46 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 720 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 1URH · The "Rhodanese" fold and catalytic mechanism of 3-mercaptopyruvate sulfotransferases… · the same entry in another collection · chain A against A, TM-score 1.00
- P31142 · AlphaFold monomer V2.0 prediction for 3-mercaptopyruvate sulfurtransferase (P31142) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P31142
- Elsewhere: RCSB PDB 1URH · PDBe 1URH · UniProt P31142
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