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Crystal structure of heparin lyase I H151A mutant complexed with a dodecasaccharide heparin

Analyse Crystal structure of heparin lyase I H151A mutant complexed with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3INA
Type: protein
Length: 370 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heparin lyase I
Ligands: SUS, IDS, SGN, CA
Pockets: 2 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 9% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heparin lyase I	protein	370	9% helix, 48% strand	—

Ligands and binding sites

SUS · 2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · ligand · chains A
IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · 4 copies · chains A
SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 3 copies · chains A
CA · Calcium ion · metal · 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	745	0.74	0.79	64	IDS, SGN, SUS
2	142	0.40	0.73	18	empty

Compared structures

3INA · Crystal structure of heparin lyase I H151A mutant complexed with a dodecasaccharide… · 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 3INA · PDBe 3INA

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