MolNFT v1 · #117587 · protein

Crystal structure of FIN219-FIP1 complex with ja, leu and ATP

5ECN · Jasmonic acid-amido synthetase JAR1: “Crystal structure of FIN219-FIP1 complex with ja, leu and ATP”. X-ray diffraction, 4 ligands (GSH, JAA, LEU), 20 pockets (best druggability 0.83). MolNFT v1 #117587 on GenesisL1: 3D structure…

PDB: 5ECN
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, ATP
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Jasmonic acid-amido synthetase JAR1 (EC 6.3.2.-)	protein	569	39% helix, 19% 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
ATP · Adenosine-5'-triphosphate · 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, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	392	0.83	0.91	55	JAA, LEU, ATP
2	342	0.81	0.90	55	JAA, LEU, ATP
3	684	0.79	0.84	86	GSH
4	850	0.74	0.78	71	GSH
5	307	0.68	0.82	36	empty

Interfaces

6 interfaces between chains.

C–D · 1244 Å² buried · 37 hydrogen bonds · protein-protein
E–F · 1121 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 866 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 838 Å² buried · 16 hydrogen bonds · protein-protein
D–E · 804 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

5ECN · Crystal Structure of FIN219-FIP1 complex with JA, Leu and ATP · 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 E 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 5ECN · PDBe 5ECN · UniProt Q9SKE2 · UniProt Q8L7C9

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