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ADPG2 - endopolygalacturonase from arabidopsis thaliana

Analyse ADPG2 - endopolygalacturonase 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: 7B8B
Type: protein
Length: 736 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polygalacturonase ADPG2
EC: 3.2.1.15
UniProt: Q8RY29
Ligands: PO4
Pockets: 7 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Polygalacturonase ADPG2 (EC 3.2.1.15)	protein	369	8% helix, 54% strand	Q8RY29
B	Polygalacturonase ADPG2 (EC 3.2.1.15)	protein	367	7% helix, 53% strand	Q8RY29

Ligands and binding sites

PO4 · Phosphate ion · ion · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	234	0.52	0.76	43	PO4
2	185	0.50	0.77	29	empty
3	170	0.47	0.76	34	empty
4	61	0.41	0.81	20	empty
5	71	0.34	0.76	20	empty

Interfaces

1 interface between chains.

A–B · 1674 Å² buried · 41 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

7B8B · ADPG2 - endopolygalacturonase from arabidopsis thaliana · the same entry in another collection · chain A against A, TM-score 1.00
Q8RY29 · AlphaFold monomer V2.0 prediction for polygalacturonase ADPG2 (Q8RY29) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q8RY29
Elsewhere: RCSB PDB 7B8B · PDBe 7B8B · UniProt Q8RY29

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