MolNFT v1 · #66208 · protein
Crystal structure of human glutathione transferase pi Y108V mutant
3HJM · Glutathione S-transferase P: “Crystal structure of human glutathione transferase pi Y108V mutant”. X-ray diffraction, 4 ligands (CA, CO3, CL), 8 pockets (best druggability 0.72). MolNFT v1 #66208 on GenesisL1: 3D structure, binding…
- PDB
- 3HJM
- Type
- protein
- Length
- 832 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione S-transferase P
- EC
- 2.5.1.18
- UniProt
- P09211
- Ligands
- CA, CO3, CL, PO4
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 62% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glutathione S-transferase P (EC 2.5.1.18) | protein | 208 | 62% helix, 8% strand | P09211 |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains A, B, C, D
- CO3 · Carbonate ion · ion · 5 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · chains D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, B, D
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 | 700 | 0.72 | 0.78 | 90 | CO3, CL |
| 2 | 615 | 0.71 | 0.79 | 77 | CO3, CL |
| 3 | 530 | 0.68 | 0.78 | 55 | empty |
| 4 | 66 | 0.68 | 0.95 | 21 | empty |
| 5 | 76 | 0.35 | 0.75 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1308 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1305 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 272 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 185 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 100 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3HJM · Crystal structure of human Glutathione Transferase Pi Y108V mutant · 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 3HJM · PDBe 3HJM · UniProt P09211
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