MolNFT v1 · #138667 · protein
Crystal structure of 3-mercaptopyruvate SULFURTRANSFERASE(3MST) in complex with COMPOUND1
5WQK: “Crystal structure of 3-mercaptopyruvate SULFURTRANSFERASE(3MST) in complex with COMPOUND1”. X-ray diffraction, 2 ligands (7NC, NA), 4 pockets (best druggability 0.66). MolNFT v1 #138667 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5WQK
- Type
- protein
- Length
- 585 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sulfurtransferase
- UniProt
- Q505N7
- Ligands
- 7NC, NA
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sulfurtransferase | protein | 293 | 34% helix, 13% strand | Q505N7 |
| B | Sulfurtransferase | protein | 292 | 35% helix, 13% strand | Q505N7 |
Ligands and binding sites
- 7NC · 4-methyl-2-(2-naphthalen-1-yl-2-oxidanylidene-ethyl) sulfanyl-1~{H}-pyrimidin-6-one · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 626 | 0.66 | 0.76 | 53 | empty |
| 2 | 206 | 0.57 | 0.80 | 38 | 7NC |
| 3 | 220 | 0.56 | 0.79 | 38 | 7NC |
| 4 | 55 | 0.25 | 0.72 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 317 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 5WQK · Crystal structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in complex with compound1 · the same entry in another collection · 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 Q505N7
- Elsewhere: RCSB PDB 5WQK · PDBe 5WQK · UniProt Q505N7
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