1JMJ Blood Clotting date Jul 18, 2001
title Crystal Structure Of Native Heparin Cofactor II
authors T.P.Baglin, R.W.Carrell, F.C.Church, J.A.Huntington
compound source
Molecule: Heparin Cofactor II
Chain: A, B
Synonym: Hc-II; Protease Inhibitor Leuserpin 2; Hls2; Serin Cysteine) Proteinase Inhibitor, Clade D (Heparin Cofactor),
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1 21 1
R_factor 0.208 R_Free 0.255
length a length b length c angle alpha angle beta angle gamma
74.730 80.000 92.240 90.00 102.04 90.00
method X-Ray Diffractionresolution 2.35 Å
ligand BMA, CA, NAG enzyme
related structures by homologous chain: 1JMO
A, B

Primary referenceCrystal structures of native and thrombin-complexed heparin cofactor II reveal a multistep allosteric mechanism., Baglin TP, Carrell RW, Church FC, Esmon CT, Huntington JA, Proc Natl Acad Sci U S A 2002 Aug 20;99(17):11079-84. PMID:12169660
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (139 Kb) [Save to disk]
  • Biological Unit Coordinates (1jmj.pdb1.gz) 134 Kb
  • LPC: Ligand-Protein Contacts for 1JMJ
  • CSU: Contacts of Structural Units for 1JMJ
  • Likely Quarternary Molecular Structure file(s) for 1JMJ
  • Structure Factors (397 Kb)
  • Retrieve 1JMJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1JMJ from S2C, [Save to disk]
  • Re-refined 1jmj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1JMJ 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 1JMJ
  • 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 1JMJ, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1jmja_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1jmjb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1jmj from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1jmj_B] [1jmj_A] [1jmj]
  • SWISS-PROT database: [P05546]
  • Domain organization of [HEP2_HUMAN] by SWISSPFAM
  • Domain found in 1JMJ: [SERPIN ] by SMART
  • Other resources with information on 1JMJ
  • Community annotation for 1JMJ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 1JMJ from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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