Research workbench
Crystal structure of MGSTA1-1 in complex with glutathione conjugate of BENZO[A]PYRENE epoxide
Analyse Crystal structure of MGSTA1-1 in complex with glutathione conjugate of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F3B
- Type
- protein
- Length
- 444 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione S-transferase ya chain
- EC
- 2.5.1.18
- UniProt
- P13745
- Ligands
- GBX
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 60% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutathione S-transferase ya chain (EC 2.5.1.18) | protein | 222 | 60% helix, 8% strand | P13745 |
Ligands and binding sites
- GBX · 2-amino-4-[1-(carboxymethyl-carbamoyl)-2-(9-hydroxy-7,8-dioxo-7,8,9,10-tetrahydro-benzo[def]chrysen-10-ylsulfanyl)-ethylcarbamoyl]-butyric acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 668 | 0.80 | 0.84 | 77 | GBX |
| 2 | 416 | 0.75 | 0.84 | 48 | GBX |
| 3 | 149 | 0.41 | 0.74 | 25 | empty |
| 4 | 113 | 0.37 | 0.74 | 19 | empty |
| 5 | 62 | 0.30 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1712 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 1F3B · Crystal structure of MGSTA1-1 in complex with glutathione conjugate of BENZO[A]PYRENE… · the same entry in another collection · chain A against A, TM-score 1.00
- P13745 · AlphaFold monomer V2.0 prediction for glutathione S-transferase A1 (P13745) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P13745
- Elsewhere: RCSB PDB 1F3B · PDBe 1F3B · UniProt P13745
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.