MolNFT v1 · #117586 · protein
Crystal structure of FIN219-FIP1 complex with ja and leu
5ECM · Jasmonic acid-amido synthetase JAR1: “Crystal structure of FIN219-FIP1 complex with ja and leu”. X-ray diffraction, 3 ligands (GSH, JAA, LEU), 20 pockets (best druggability 0.84). MolNFT v1 #117586 on GenesisL1: 3D structure…
- PDB
- 5ECM
- 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, LEU
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Jasmonic acid-amido synthetase JAR1 (EC 6.3.2.-) | protein | 569 | 38% helix, 18% strand | Q9SKE2 |
| B, C, E, F | Glutathione S-transferase U20 (EC 2.5.1.18) | protein | 214 | 55% helix, 8% 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
- LEU · Leucine · ligand · 2 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.84 | 0.96 | 44 | JAA, LEU |
| 2 | 216 | 0.83 | 0.96 | 39 | JAA, LEU |
| 3 | 1003 | 0.76 | 0.78 | 72 | GSH |
| 4 | 1012 | 0.76 | 0.78 | 70 | GSH |
| 5 | 328 | 0.67 | 0.81 | 32 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1205 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1043 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1009 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 901 Ų buried · 31 hydrogen bonds · protein-protein
- D–E · 901 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5ECM · Crystal Structure of FIN219-FIP1 complex with JA and Leu · the same entry in another collection · chain D against D, TM-score 1.00
- Q8L7C9 · AlphaFold monomer V2.0 prediction for glutathione S-transferase U20 (Q8L7C9) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q9SKE2 · AlphaFold monomer V2.0 prediction for jasmonoyl--L-amino acid synthetase JAR1 (Q9SKE2) · a predicted model of the same protein · chain D 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 5ECM · PDBe 5ECM · UniProt Q9SKE2 · UniProt Q8L7C9
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