1JMO Blood Clotting date Jul 19, 2001
title Crystal Structure Of The Heparin Cofactor II-S195a Thrombin
authors T.P.Baglin, R.W.Carrell, C.T.Esmon, J.A.Huntington
compound source
Molecule: Thrombin, Light Chain
Chain: L
Fragment: Light Chain
Synonym: Coagulation Factor II
Engineered: Yes
Other_details: Contains Extra 13 Amino Acids At The N-Termi
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell_line: Bhk Culture
Expression_system_organ: Kidney

Molecule: Thrombin, Heavy Chain
Chain: H
Fragment: Heavy Chain
Synonym: Coagulation Factor II
Ec: 3.4.21.5
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell_line: Bhk Culture
Expression_system_organ: Kidney

Molecule: Heparin Cofactor II
Chain: A
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
Other_details: Plasma Purified Human Heparin Cofactor II
symmetry Space Group: P 61
R_factor 0.205 R_Free 0.211
crystal
cell
length a length b length c angle alpha angle beta angle gamma
152.310 152.310 126.800 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.20 Å
ligand MPD, NA, NAG, NDG, TYS enzyme Hydrolase E.C.3.4.21.5 BRENDA
related structures by homologous chain: 1JMJ, 1NU7, 1QHR
Gene
Ontology
ChainFunctionProcessComponent
A


H


L


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] (132 Kb) [Save to disk]
  • Biological Unit Coordinates (1jmo.pdb1.gz) 126 Kb
  • LPC: Ligand-Protein Contacts for 1JMO
  • CSU: Contacts of Structural Units for 1JMO
  • Likely Quarternary Molecular Structure file(s) for 1JMO
  • Structure Factors (773 Kb)
  • Retrieve 1JMO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1JMO from S2C, [Save to disk]
  • Re-refined 1jmo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1JMO 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 1JMO
  • 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 1JMO, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1jmoa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1jmo.1, region L:,H [Jmol] [rasmolscript] [script source]
  • Fold representative 1jmo 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: [1jmo_L] [1jmo_H] [1jmo_A] [1jmo]
  • SWISS-PROT database: [P05546] [P00734]
  • Domain organization of [HEP2_HUMAN] [THRB_HUMAN] by SWISSPFAM
  • Domains found in 1JMO: [SERPIN] [Tryp_SPc ] by SMART
  • Other resources with information on 1JMO
  • Community annotation for 1JMO 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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