5E8M Hydrolase date Oct 14, 2015
title Crystal Structure Of Human Heparanase
authors L.Wu, G.J.Davies
compound source
Molecule: Heparanase
Chain: A
Fragment: Unp Residues 158-543
Synonym: Endo-Glucoronidase,Heparanase-1,Hpa1, Glycoside Hy
Ec: 3.2.1.166
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hpse, Hep, Hpa, Hpa1, Hpr1, Hpse1, Hse1
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Heparanase
Chain: B
Fragment: Unp Residues 36-109
Synonym: Endo-Glucoronidase,Heparanase-1,Hpa1, Glycoside Hy
Ec: 3.2.1.166
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hpse, Hep, Hpa, Hpa1, Hpr1, Hpse1, Hse1
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
symmetry Space Group: P 1 21 1
R_factor 0.164 R_Free 0.200
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.765 70.972 78.948 90.00 94.17 90.00
method X-Ray Diffractionresolution 1.75 Å
ligand CL, EDO, FUC, NAG enzyme Hydrolase E.C.3.2.1.166 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural characterization of human heparanase reveals insights into substrate recognition., Wu L, Viola CM, Brzozowski AM, Davies GJ, Nat Struct Mol Biol. 2015 Nov 16. doi: 10.1038/nsmb.3136. PMID:26575439
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (88 Kb) [Save to disk]
  • Biological Unit Coordinates (5e8m.pdb1.gz) 82 Kb
  • LPC: Ligand-Protein Contacts for 5E8M
  • CSU: Contacts of Structural Units for 5E8M
  • Structure Factors (3494 Kb)
  • Retrieve 5E8M in mmCIF format [Save to disk]
  • Re-refined 5e8m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5E8M in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 5E8M
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5e8m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5e8m_B] [5e8m_A] [5e8m]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5E8M
  • Community annotation for 5E8M at PDBWiki (http://pdbwiki.org)

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