4DY7 Hydrolase Hydrolase Inhibitor date Feb 28, 2012
title Crystal Structures Of Protease Nexin-1 In Complex With S195a
authors J.A.Huntington, W.Li
compound source
Molecule: Thrombin Light Chain
Chain: A, D
Fragment: Unp Residues 315-363
Ec: 3.4.21.5
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: F2
Expression_system: Cricetinae Gen. Sp.
Expression_system_taxid: 36483
Expression_system_organ: Kidney
Expression_system_cell: Baby Hamster Kidney (Bhk) Cells

Molecule: Thrombin Heavy Chain
Chain: B, E
Ec: 3.4.21.5
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: F2
Expression_system: Cricetinae Gen. Sp.
Expression_system_taxid: 36483
Expression_system_organ: Kidney
Expression_system_cell: Baby Hamster Kidney (Bhk) Cells

Molecule: Glia-Derived Nexin
Chain: C, F
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: C 1 2 1
R_factor 0.223 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
191.960 86.670 101.890 90.00 94.44 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand ACT, CA, NA enzyme Hydrolase E.C.3.4.21.5 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D


E, B


F, C
  • 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] (211 Kb) [Save to disk]
  • Biological Unit Coordinates (4dy7.pdb1.gz) 106 Kb
  • Biological Unit Coordinates (4dy7.pdb2.gz) 101 Kb
  • LPC: Ligand-Protein Contacts for 4DY7
  • CSU: Contacts of Structural Units for 4DY7
  • Structure Factors (615 Kb)
  • Retrieve 4DY7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DY7 from S2C, [Save to disk]
  • Re-refined 4dy7 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DY7 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 4DY7
  • 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 4DY7, from MSDmotif at EBI
  • Fold representative 4dy7 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dy7_F] [4dy7_B] [4dy7_E] [4dy7_C] [4dy7_A] [4dy7_D] [4dy7]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4DY7: [SERPIN] [Tryp_SPc ] by SMART
  • Other resources with information on 4DY7
  • Community annotation for 4DY7 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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