Research workbench
Structure and kinetic analysis of H2S production by human mercaptopyruvate sulfurtransferase
Analyse Structure and kinetic analysis of H2S production by human mercaptopyruvate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JGT
- Type
- protein
- Length
- 835 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-mercaptopyruvate sulfurtransferase
- EC
- 2.8.1.2
- UniProt
- P25325
- Ligands
- PYR, SO4
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-mercaptopyruvate sulfurtransferase (EC 2.8.1.2) | protein | 280 | 34% helix, 13% strand | P25325 |
| B | 3-mercaptopyruvate sulfurtransferase (EC 2.8.1.2) | protein | 278 | 35% helix, 13% strand | P25325 |
| C | 3-mercaptopyruvate sulfurtransferase (EC 2.8.1.2) | protein | 277 | 34% helix, 13% strand | P25325 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1172 | 0.74 | 0.77 | 101 | PYR |
| 2 | 100 | 0.71 | 0.94 | 37 | empty |
| 3 | 115 | 0.46 | 0.78 | 25 | PYR |
| 4 | 89 | 0.41 | 0.78 | 14 | empty |
| 5 | 67 | 0.39 | 0.79 | 20 | PYR |
Interfaces
3 interfaces between chains.
- A–C · 731 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 570 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 231 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (oxidation).
Compared structures
- 4JGT · Structure and kinetic analysis of H2S production by human Mercaptopyruvate… · the same entry in another collection · chain A against A, TM-score 1.00
- P25325 · AlphaFold monomer V2.0 prediction for 3-mercaptopyruvate sulfurtransferase (P25325) · 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 P25325
- Elsewhere: RCSB PDB 4JGT · PDBe 4JGT · UniProt P25325
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