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Rhamnogalacturonase a from aspergillus aculeatus

Analyse Rhamnogalacturonase a from aspergillus aculeatus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1RMG
Type: protein
Length: 422 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rhamnogalacturonase a
EC: 3.2.1.-
Ligands: MAN, BMA, NAG, GLC
Pockets: 1 · best druggability 0.27

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rhamnogalacturonase a (EC 3.2.1.-)	protein	422	6% helix, 51% strand	—

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 15 copies · chains A
BMA · beta-D-mannopyranose · sugar · 6 copies · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
GLC · alpha-D-glucopyranose · sugar · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	51	0.27	0.75	13	empty

Modifications

Observed in the structure: 20 glycan, 4 disulfide (O-glycosylation, disulfide, N-glycosylation).

Compared structures

1RMG · Rhamnogalacturonase a from aspergillus aculeatus · 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
Elsewhere: RCSB PDB 1RMG · PDBe 1RMG

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