3KCG Hydrolase, Hydrolase Inhibitor date Oct 21, 2009
title Crystal Structure Of The Antithrombin-Factor Ixa-Pentasaccha Complex
authors J.A.Huntington, D.J.D.Johnson
compound source
Molecule: Coagulation Factor Ixa Light Chain
Chain: L
Fragment: Egf2
Synonym: Factor Ix, Christmas Factor, Plasma Thromboplastin Component, Ptc;
Ec: 3.4.21.22
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: F9
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Coagulation Factor Ixa Heavy Chain
Chain: H
Synonym: Factor Ix, Christmas Factor, Plasma Thromboplastin Component, Ptc;
Ec: 3.4.21.22
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: F9
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Antithrombin-III
Chain: I
Synonym: Atiii
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Serpinc1, At3, Pro0309
Expression_system_cell: Bhk
symmetry Space Group: P 21 21 21
R_factor 0.208 R_Free 0.230
crystal
cell
length a length b length c angle alpha angle beta angle gamma
78.780 88.440 147.230 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand CA, FUC, GU1, GU6, MAN, MPD, NAG, Z9H, Z9K, Z9L enzyme Hydrolase E.C.3.4.21.22 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
H


I


L


Primary referenceMolecular basis of factor IXa recognition by heparin-activated antithrombin revealed by a 1.7-A structure of the ternary complex., Johnson DJ, Langdown J, Huntington JA, Proc Natl Acad Sci U S A. 2010 Jan 12;107(2):645-50. Epub 2009 Dec 22. PMID:20080729
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (141 Kb) [Save to disk]
  • Biological Unit Coordinates (3kcg.pdb1.gz) 134 Kb
  • LPC: Ligand-Protein Contacts for 3KCG
  • CSU: Contacts of Structural Units for 3KCG
  • Structure Factors (828 Kb)
  • Retrieve 3KCG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KCG from S2C, [Save to disk]
  • Re-refined 3kcg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3KCG 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 3KCG
  • 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
  • 3D motif for 3KCG, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3kcg_I] [3kcg_L] [3kcg_H] [3kcg]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3KCG: [EGF] [SERPIN] [Tryp_SPc ] by SMART
  • Other resources with information on 3KCG
  • Community annotation for 3KCG at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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