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Crystal structure of a glutathione transferase family member from psuedomonas fluorescens pf-5, target efi-900011, with bound S- (propanoic acid)-glutathione
Analyse Crystal structure of a glutathione transferase family member from psuedomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IJI
- Type
- protein
- Length
- 1,598 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione S-transferase-like protein yibf
- UniProt
- Q4K4R5
- Ligands
- 99T, BEZ, AKR
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 59% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, G | Glutathione S-transferase-like protein yibf | protein | 204 | 59% helix, 8% strand | Q4K4R5 |
| C | Glutathione S-transferase-like protein yibf | protein | 195 | 59% helix, 7% strand | Q4K4R5 |
| D | Glutathione S-transferase-like protein yibf | protein | 203 | 59% helix, 7% strand | Q4K4R5 |
| E | Glutathione S-transferase-like protein yibf | protein | 196 | 60% helix, 9% strand | Q4K4R5 |
| F | Glutathione S-transferase-like protein yibf | protein | 198 | 57% helix, 8% strand | Q4K4R5 |
| H | Glutathione S-transferase-like protein yibf | protein | 194 | 60% helix, 8% strand | Q4K4R5 |
Ligands and binding sites
- 99T · L-gamma-glutamyl-S-(2-carboxyethyl)-L-cysteinylglycine · ligand · 6 copies · chains A, F, B, C, D, H, E, G
- BEZ · Benzoic acid · ligand · 2 copies · chains F, H
- AKR · Acrylic acid · ligand · 2 copies · chains F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.87 | 0.87 | 86 | 99T, BEZ, AKR |
| 2 | 941 | 0.86 | 0.87 | 78 | 99T |
| 3 | 1044 | 0.85 | 0.86 | 88 | 99T |
| 4 | 975 | 0.82 | 0.83 | 119 | empty |
| 5 | 947 | 0.81 | 0.83 | 76 | 99T, BEZ, AKR |
Interfaces
15 interfaces between chains.
- A–F · 2178 Ų buried · 36 hydrogen bonds · protein-protein
- E–G · 2091 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 2035 Ų buried · 33 hydrogen bonds · protein-protein
- D–H · 1932 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 506 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 4IJI · Crystal structure of a glutathione transferase family member from Psuedomonas fluorescens… · 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 Q4K4R5
- Elsewhere: RCSB PDB 4IJI · PDBe 4IJI · UniProt Q4K4R5
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