Research workbench
Crystal structure of FIN219-FIP1 complex with ja, ile and mg
Analyse Crystal structure of FIN219-FIP1 complex with ja, ile and mg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ECL
- Type
- protein
- Length
- 1,994 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Jasmonic acid-amido synthetase JAR1; Glutathione S-transferase U20
- EC
- 6.3.2.-, 2.5.1.18
- UniProt
- Q9SKE2, Q8L7C9
- Ligands
- GSH, JAA, ILE, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Jasmonic acid-amido synthetase JAR1 (EC 6.3.2.-) | protein | 569 | 38% helix, 16% strand | Q9SKE2 |
| B, C, E, F | Glutathione S-transferase U20 (EC 2.5.1.18) | protein | 214 | 58% helix, 7% strand | Q8L7C9 |
Ligands and binding sites
- GSH · Glutathione · ligand · 4 copies · chains B, C, E, F
- JAA · {(1R,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetic acid · ligand · 2 copies · chains A, D
- ILE · Isoleucine · ligand · 2 copies · chains A, D
- MG · Magnesium ion · metal · 4 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.84 | 0.94 | 43 | JAA, ILE, MG |
| 2 | 418 | 0.84 | 0.92 | 69 | JAA, ILE, MG |
| 3 | 1020 | 0.79 | 0.80 | 106 | GSH |
| 4 | 457 | 0.69 | 0.80 | 46 | GSH |
| 5 | 248 | 0.60 | 0.79 | 33 | empty |
Interfaces
7 interfaces between chains.
- D–E · 1171 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1153 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 1121 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1113 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 880 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5ECL · Crystal Structure of FIN219-FIP1 complex with JA, Ile and Mg · the same entry in another collection · chain F against F, TM-score 1.00
- Q8L7C9 · AlphaFold monomer V2.0 prediction for glutathione S-transferase U20 (Q8L7C9) · a predicted model of the same protein · chain F against A, TM-score 0.97
- 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 0.74
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 Q8L7C9
- Elsewhere: RCSB PDB 5ECL · PDBe 5ECL · UniProt Q9SKE2 · UniProt Q8L7C9
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