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Arabidopsis GH3.12 with chorismate

Analyse Arabidopsis GH3.12 with chorismate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6OMS
Type: protein
Length: 979 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 4-substituted benzoates-glutamate ligase GH3.12
EC: 6.3.2.-
UniProt: Q9LYU4
Ligands: AMP, ISJ
Pockets: 7 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	4-substituted benzoates-glutamate ligase GH3.12 (EC 6.3.2.-)	protein	487	43% helix, 22% strand	Q9LYU4
B	4-substituted benzoates-glutamate ligase GH3.12 (EC 6.3.2.-)	protein	492	43% helix, 22% strand	Q9LYU4

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
ISJ · (3R,4R)-3-[(1-carboxyethenyl)oxy]-4-hydroxycyclohexa-1, 5-diene-1-carboxylic acid · ligand · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	803	0.86	0.89	82	AMP
2	827	0.86	0.89	80	AMP, ISJ
3	443	0.67	0.79	44	empty
4	97	0.51	0.83	26	empty
5	144	0.49	0.79	27	empty

Interfaces

1 interface between chains.

A–B · 1053 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

6OMS · Arabidopsis GH3.12 with Chorismate · the same entry in another collection · chain A against A, TM-score 1.00
Q9LYU4 · AlphaFold monomer V2.0 prediction for 4-substituted benzoates- glutamate ligase GH3.12… · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q9LYU4
Elsewhere: RCSB PDB 6OMS · PDBe 6OMS · UniProt Q9LYU4

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