4DY0 Hydrolase Inhibitor date Feb 28, 2012
title Crystal Structure Of Native Protease Nexin-1 With Heparin
authors J.A.Huntington, W.Li
compound source
Molecule: Glia-Derived Nexin
Chain: A, B
Synonym: Gdn, Peptidase Inhibitor 7, Pi-7, Protease Nexin 1 Protease Nexin I, Serpin E2;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Serpine2, Pi7, Pn1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 41 21 2
R_factor 0.182 R_Free 0.226
length a length b length c angle alpha angle beta angle gamma
140.650 140.650 93.550 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.35 Å
ligand GOL, IDS, SGN, SO4 enzyme
A, B
  • serine-type endopeptidase in...

  • Primary referenceCrystal structures of protease nexin-1 in complex with heparin and thrombin suggest a 2-step recognition mechanism., Li W, Huntington JA, Blood. 2012 Jul 12;120(2):459-67. Epub 2012 May 22. PMID:22618708
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (243 Kb) [Save to disk]
  • Biological Unit Coordinates (4dy0.pdb1.gz) 116 Kb
  • Biological Unit Coordinates (4dy0.pdb2.gz) 120 Kb
  • Biological Unit Coordinates (4dy0.pdb3.gz) 234 Kb
  • Biological Unit Coordinates (4dy0.pdb4.gz) 235 Kb
  • LPC: Ligand-Protein Contacts for 4DY0
  • CSU: Contacts of Structural Units for 4DY0
  • Structure Factors (575 Kb)
  • Retrieve 4DY0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DY0 from S2C, [Save to disk]
  • Re-refined 4dy0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DY0 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 4DY0
  • 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
  • 3D motif for 4DY0, from MSDmotif at EBI
  • Fold representative 4dy0 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dy0] [4dy0_A] [4dy0_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4DY0: [SERPIN ] by SMART
  • Other resources with information on 4DY0
  • Community annotation for 4DY0 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • 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