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Crystal structure of arabidopsis GH3.12 (PBS3) in complex with AMP

Analyse Crystal structure of arabidopsis GH3.12 (PBS3) in complex with AMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4EPM
Type: protein
Length: 554 residues
Chains: 1
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, SO4
Pockets: 1 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 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	554	43% helix, 22% strand	Q9LYU4

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · chains A
SO4 · Sulfate ion · ion · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1056	0.85	0.86	111	AMP, SO4

Compared structures

4EPM · Crystal Structure of Arabidopsis GH3.12 (PBS3) in Complex with AMP · 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 0.95

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 4EPM · PDBe 4EPM · UniProt Q9LYU4

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