Research workbench
Crystal structure of FIN219-sjgst complex with ja
Analyse Crystal structure of FIN219-sjgst complex with ja in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GZZ
- Type
- protein
- Length
- 1,865 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Jasmonic acid-amido synthetase JAR1; Glutathione S-transferase class-mu 26 kda isozyme
- EC
- 6.3.2.-, 2.5.1.18
- UniProt
- Q9SKE2, P08515
- Ligands
- GSH, JAA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Jasmonic acid-amido synthetase JAR1 (EC 6.3.2.-) | protein | 569 | 38% helix, 17% strand | Q9SKE2 |
| B, C, D, E, F, G | Glutathione S-transferase class-mu 26 kda isozyme (EC 2.5.1.18) | protein | 216 | 48% helix, 8% strand | P08515 |
Ligands and binding sites
- GSH · Glutathione · ligand · 6 copies · chains B, C, D, E, F, G
- JAA · {(1R,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.85 | 0.85 | 122 | GSH |
| 2 | 839 | 0.82 | 0.84 | 108 | JAA |
| 3 | 966 | 0.78 | 0.80 | 86 | empty |
| 4 | 821 | 0.77 | 0.80 | 69 | GSH |
| 5 | 676 | 0.75 | 0.81 | 65 | GSH |
Interfaces
7 interfaces between chains.
- F–G · 1704 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 1641 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1326 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1261 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1032 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5GZZ · Crystal Structure of FIN219-SjGST complex with JA · the same entry in another collection · chain D against D, TM-score 1.00
- P08515 · AlphaFold monomer V2.0 prediction for glutathione S-transferase class-mu 26 kda isozyme… · a predicted model of the same protein · chain B against A, TM-score 0.94
- Q9SKE2 · AlphaFold monomer V2.0 prediction for jasmonoyl--L-amino acid synthetase JAR1 (Q9SKE2) · a predicted model of the same protein · chain A against A, TM-score 0.73
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 Q9SKE2
- Every structure of UniProt P08515
- Elsewhere: RCSB PDB 5GZZ · PDBe 5GZZ · UniProt Q9SKE2 · UniProt P08515
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