1DZH Blood Clotting date Feb 28, 2000
title P14-Fluorescein-N135q-S380c-Antithrombin-III
authors A.J.Mccoy, J.A.Huntington, R.W.Carrell
compound source
Molecule: Antithrombin-III
Chain: I
Synonym: Atiii, Serpin C1
Engineered: Yes
Mutation: Yes
Other_details: Inhibitory Conformation Fluorescein Attached (P14);
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Cricetidae Sp.
Expression_system_taxid: 36483
Expression_system_plasmid: Pmastop
Other_details: Recombinant. Baby Hamster Kidney (Bhk) Cell Expression;

Molecule: Antithrombin-III
Chain: L
Synonym: Atiii, Serpin C1
Other_details: Latent Conformation

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Plasma Alpha Antithrombin-III
symmetry Space Group: P 1 21 1
R_factor 0.207 R_Free 0.258
length a length b length c angle alpha angle beta angle gamma
69.175 99.865 89.421 90.00 105.63 90.00
method X-Ray Diffractionresolution 2.85 Å
ligand BMA, CYF, GOL, NAG enzyme
related structures by homologous chain: 1DZG, 1E03
  • serine-type endopeptidase in...

  • L
  • serine-type endopeptidase in...

  • Primary referenceThe conformational activation of antithrombin. A 2.85-A structure of a fluorescein derivative reveals an electrostatic link between the hinge and heparin binding regions., Huntington JA, McCoy A, Belzar KJ, Pei XY, Gettins PG, Carrell RW, J Biol Chem 2000 May 19;275(20):15377-83. PMID:10809774
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (143 Kb) [Save to disk]
  • Biological Unit Coordinates (1dzh.pdb1.gz) 68 Kb
  • Biological Unit Coordinates (1dzh.pdb2.gz) 71 Kb
  • LPC: Ligand-Protein Contacts for 1DZH
  • CSU: Contacts of Structural Units for 1DZH
  • Likely Quarternary Molecular Structure file(s) for 1DZH
  • Structure Factors (251 Kb)
  • Retrieve 1DZH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DZH from S2C, [Save to disk]
  • Re-refined 1dzh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1DZH 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 1DZH
  • 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 1DZH, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dzhi_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1dzhl_, region L [Jmol] [rasmolscript] [script source]
  • Fold representative 1dzh 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: [1dzh_L] [1dzh_I] [1dzh]
  • SWISS-PROT database: [P01008]
  • Domain organization of [ANT3_HUMAN] by SWISSPFAM
  • Domain found in 1DZH: [SERPIN ] by SMART
  • Other resources with information on 1DZH
  • Community annotation for 1DZH 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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