6ZDM: Crystal structure of human heparanase in complex with a N',6O'-bis-sulfated 4-methylumbelliferyl heparan sulfate disaccharide

PDB ID: 6ZDMDownload
MMDB ID: 199751
PDB Deposition Date: 2020/6/14
Updated in MMDB: 2021/03
Experimental Method:
x-ray diffraction
Resolution: 1.714  Å
Source Organism:
Similar Structures:
Biological Unit for 6ZDM: dimeric; determined by author and by software (PISA)
Molecular Components in 6ZDM
Label Count Molecule
Proteins (2 molecules)
1
Heparanase
(Gene symbol: HPSE)
Molecule annotation
1
Heparanase
(Gene symbol: HPSE)
Molecule annotation
Chemicals and Non-standard biopolymers (8 molecules)
1
1
2-acetamido-2-deoxy-beta-D-glucopyranose2-acetamido-2-deoxy-beta-D-glucopyranose
2
1
1,2-ETHANEDIOL1,2-ETHANEDIOL
3
1
(2~{S},3~{S},4~{R},5~{R},6~{S})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-4,5-bis(oxidanyl)-3-(sulfoamino)-6-(sulfooxymethyl)oxan-2-yl]oxy-6-(4-methyl-2-oxidanylidene-chromen-7-yl)oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid(2~{S},3~{S},4~{R},5~{R},6~{S})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-4,5-bis(oxidanyl)-3-(sulfoamino)-6-(sulfooxymethyl)oxan-2-yl]oxy-6-(4-methyl-2-oxidanylidene-chromen-7-yl)oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid
4
5
SULFATE IONSULFATE ION
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303