MolNFT v2 · #116924 · protein
Structure of WT Human Glutathione Transferase in complex with cisplatin in the absence of glutathione.
5DJM · Glutathione S-transferase P: “Structure of WT Human Glutathione Transferase in complex with cisplatin in the absence of glutathione.”. X-ray diffraction at 1.9, 1 ligand (PT), 3 pockets (best druggability 0.74). MolNFT v2 #116924 on…
- PDB
- 5DJM
- Type
- protein
- Length
- 396 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Homo sapiens
- Molecule
- Glutathione S-transferase P
- EC
- 2.5.1.18
- UniProt
- P09211
- Ligands
- PT
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · resolution 1.9 · 2 distinct chains · 59% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutathione S-transferase P (EC 2.5.1.18) | protein | 199 | 59% helix, 9% strand | P09211 |
| B | Glutathione S-transferase P (EC 2.5.1.18) | protein | 197 | 59% helix, 9% strand | P09211 |
Ligands and binding sites
- PT · Platinum (II) ion · metal · 3 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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 620 | 0.74 | 0.81 | 72 | PT |
| 2 | 93 | 0.38 | 0.76 | 19 | empty |
| 3 | 52 | 0.29 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1298 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5DJM · Structure of wt human glutathione transferase in complex with cisplatin in the absence of… · the same entry in another collection · chain A against A, TM-score 1.00
- P09211 · AlphaFold monomer V2.0 prediction for glutathione S-transferase P (P09211) · a predicted model of the same protein · chain B 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 5DJM · PDBe 5DJM · UniProt P09211
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