Research workbench
Crystal structure of HGSTP1-1[V104] complexed with the gsh conjugate of (+)-anti-bpde
Analyse Crystal structure of HGSTP1-1[V104] complexed with the gsh conjugate of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PGT
- Type
- protein
- Length
- 419 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (glutathione S-transferase)
- EC
- 2.5.1.18
- UniProt
- P09211
- Ligands
- GBX, SO4
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (glutathione S-transferase) (EC 2.5.1.18) | protein | 210 | 62% helix, 8% strand | P09211 |
| B | Protein (glutathione S-transferase) (EC 2.5.1.18) | protein | 209 | 60% helix, 9% strand | P09211 |
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
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 599 | 0.72 | 0.80 | 78 | GBX |
| 2 | 84 | 0.36 | 0.75 | 16 | empty |
| 3 | 74 | 0.35 | 0.75 | 12 | empty |
| 4 | 72 | 0.31 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1313 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 4PGT · Crystal structure of HGSTP1-1[V104] complexed with the gsh conjugate of (+)-anti-bpde · 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 P09211
- Elsewhere: RCSB PDB 4PGT · PDBe 4PGT · UniProt P09211
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