MolNFT v1 · #70727 · protein
Crystal structure of glutathione S-transferase from rhodobacter sphaeroides
3LSZ: “Crystal structure of glutathione S-transferase from rhodobacter sphaeroides”. X-ray diffraction, 1 ligand (GSH), 8 pockets (best druggability 0.77). MolNFT v1 #70727 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3LSZ
- Type
- protein
- Length
- 874 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione S-transferase
- UniProt
- Q3IZT6
- Ligands
- GSH
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 56% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutathione S-transferase | protein | 223 | 53% helix, 7% strand | Q3IZT6 |
| B | Glutathione S-transferase | protein | 220 | 59% helix, 7% strand | Q3IZT6 |
| C | Glutathione S-transferase | protein | 217 | 56% helix, 7% strand | Q3IZT6 |
| D | Glutathione S-transferase | protein | 214 | 55% helix, 7% strand | Q3IZT6 |
Ligands and binding sites
- GSH · Glutathione · ligand · 4 copies · chains A, C, B, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, C, B, D
- GOL · Glycerol · additive · 2 copies · chains 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 952 | 0.77 | 0.80 | 89 | GSH, GOL |
| 2 | 594 | 0.75 | 0.82 | 49 | GSH |
| 3 | 279 | 0.66 | 0.82 | 42 | GSH |
| 4 | 126 | 0.51 | 0.80 | 18 | TRS |
| 5 | 105 | 0.51 | 0.81 | 18 | TRS |
Interfaces
5 interfaces between chains.
- A–C · 1334 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1334 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 381 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 259 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 253 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3LSZ · Crystal structure of glutathione s-transferase from Rhodobacter sphaeroides · 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 Q3IZT6
- Elsewhere: RCSB PDB 3LSZ · PDBe 3LSZ · UniProt Q3IZT6
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