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Structure of heparinase I from bacteroides thetaiotaomicron in complex with tetrasaccharide product

Analyse Structure of heparinase I from bacteroides thetaiotaomicron in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ILR
Type: protein
Length: 364 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heparin lyase I
EC: 4.2.2.7
UniProt: Q89YQ6
Ligands: IXD, SGN, CA
Pockets: 1 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heparin lyase I (EC 4.2.2.7)	protein	364	10% helix, 47% strand	Q89YQ6

Ligands and binding sites

IXD · 4-deoxy-2-O-sulfo-beta-D-erythro-hex-4-enopyranuronic acid · ligand · 2 copies · chains A
SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 2 copies · chains A
CA · Calcium ion · metal · chains A
EDO · 1,2-ethanediol · additive · 5 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	700	0.72	0.78	61	IXD, SGN

Compared structures

3ILR · Structure of Heparinase I from Bacteroides thetaiotaomicron in complex with… · 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 Q89YQ6
Elsewhere: RCSB PDB 3ILR · PDBe 3ILR · UniProt Q89YQ6

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