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Crystal structure of environmental isolated GH11 in complex with xylobiose and feruloyl-arabino-xylotriose

Analyse Crystal structure of environmental isolated GH11 in complex with xylobiose and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VGD
Type: protein
Length: 195 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ENXYN11A
EC: 3.2.1.8
Ligands: FX3, XYP, NA
Pockets: 1 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 62% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ENXYN11A (EC 3.2.1.8)	protein	195	7% helix, 62% strand	—

Ligands and binding sites

FX3 · 5-O-[(2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enoyl]-alpha-L-ribofuranose · ligand · chains A
XYP · beta-D-xylopyranose · sugar · 5 copies · chains A
NA · Sodium ion · metal · chains A
GOL · Glycerol · additive · 4 copies · 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	150	0.52	0.79	28	XYP

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

2VGD · Crystal structure of environmental isolated GH11 in complex with xylobiose and… · 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 2VGD · PDBe 2VGD

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