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Crystal structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from fusarium oxysporum 12S, L-rha complex

Analyse Crystal structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from fusarium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7ESM
Type: protein
Length: 419 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-rhamnose-alpha-1,4-D-glucuronate lyase
EC: 4.2.2.-
Ligands: NAG, BMA, MAN, RAM, NA
Pockets: 2 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	L-rhamnose-alpha-1,4-D-glucuronate lyase (EC 4.2.2.-)	protein	419	5% helix, 47% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
BMA · beta-D-mannopyranose · sugar
MAN · alpha-D-mannopyranose · sugar
RAM · alpha-L-rhamnopyranose · sugar · chains A
NA · Sodium ion · metal · chains A
ACT · Acetate ion · additive · 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	300	0.73	0.86	49	empty
2	179	0.47	0.76	23	RAM

Modifications

Observed in the structure: 1 glycan (N-glycosylation).

Compared structures

7ESM · Crystal structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 7ESM · PDBe 7ESM

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