5L9Y Hydrolase date Jun 13, 2016
title Crystal Structure Of Human Heparanase, In Complex With Glucu Configured Aziridine Probe Jjb355
authors L.Wu, Y.Jin, G.J.Davies
compound source
Molecule: Heparanase
Chain: A
Synonym: Endo-Glucoronidase,Heparanase-1,Hpa1
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
Synonym: Endo-Glucoronidase,Heparanase-1,Hpa1
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 0.179 R_Free 0.222
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.430 71.260 78.910 90.00 94.92 90.00
method X-Ray Diffractionresolution 1.88 Å
ligand
enzyme Hydrolase E.C.3.2.1.166 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceActivity-based probes for functional interrogation of retaining beta-glucuronidases., Wu L, Jiang J, Jin Y, Kallemeijn WW, Kuo CL, Artola M, Dai W, van Elk C, van Eijk M, van der Marel GA, Codee JDC, Florea BI, Aerts JMFG, Overkleeft HS, Davies GJ, Nat Chem Biol. 2017 Jun 5. doi: 10.1038/nchembio.2395. PMID:28581485
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (85 Kb) [Save to disk]
  • Biological Unit Coordinates (5l9y.pdb1.gz) 80 Kb
  • CSU: Contacts of Structural Units for 5L9Y
  • Structure Factors (2739 Kb)
  • Retrieve 5L9Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5L9Y from S2C, [Save to disk]
  • Re-refined 5l9y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5L9Y 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 5L9Y
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5l9y from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5l9y_A] [5l9y_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5L9Y
  • Community annotation for 5L9Y at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science