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Endo-polygalacturonase from arabidopsis thaliana

Analyse Endo-polygalacturonase from arabidopsis thaliana in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7B7A
Type: protein
Length: 391 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pectin lyase-like superfamily protein
UniProt: Q9LYJ5
Ligands: NAG, MAN, BMA
Pockets: 2 · best druggability 0.56

Structure

x-ray diffraction · 1 distinct chain · 8% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pectin lyase-like superfamily protein	protein	391	8% helix, 49% strand	Q9LYJ5

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A
BMA · beta-D-mannopyranose · sugar · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	298	0.56	0.77	35	empty
2	66	0.33	0.76	21	empty

Modifications

Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

7B7A · Endo-polygalacturonase from arabidopsis thaliana · the same entry in another collection · chain A against A, TM-score 1.00

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 Q9LYJ5
Elsewhere: RCSB PDB 7B7A · PDBe 7B7A · UniProt Q9LYJ5

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