1IJK Blood Clotting Toxin date Apr 26, 2001
title The Von Willebrand Factor Mutant (I546v) A1 Domain- Botrocetin Complex
authors K.Fukuda, T.A.Doggett, L.A.Bankston, M.A.Cruz, T.G.Diacovo, R.C.Liddington
compound source
Molecule: Von Willebrand Factor
Chain: A
Fragment: A1 Domain
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Botrocetin
Chain: B
Fragment: A-Subunit

Organism_scientific: Bothrops Jararaca
Organism_common: Jararaca
Organism_taxid: 8724
Secretion: Venom

Molecule: Botrocetin
Chain: C
Fragment: B-Subunit

Organism_scientific: Bothrops Jararaca
Organism_common: Jararaca
Organism_taxid: 8724
Secretion: Venom
symmetry Space Group: P 1 21 1
R_factor 0.219 R_Free 0.279
crystal
cell
length a length b length c angle alpha angle beta angle gamma
65.664 66.672 69.402 90.00 105.41 90.00
method X-Ray Diffractionresolution 2.60 Å
related structures by homologous chain: 1BJ3, 1SQ0, 1U0O, 1UMR, 1UOS
Gene
Ontology
ChainFunctionProcessComponent
C, B


Primary referenceStructural basis of von Willebrand factor activation by the snake toxin botrocetin., Fukuda K, Doggett TA, Bankston LA, Cruz MA, Diacovo TG, Liddington RC, Structure (Camb) 2002 Jul;10(7):943-50. PMID:12121649
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (81 Kb) [Save to disk]
  • Biological Unit Coordinates (1ijk.pdb1.gz) 77 Kb
  • CSU: Contacts of Structural Units for 1IJK
  • Likely Quarternary Molecular Structure file(s) for 1IJK
  • Structure Factors (298 Kb)
  • Retrieve 1IJK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1IJK from S2C, [Save to disk]
  • Re-refined 1ijk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1IJK 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 1IJK
  • 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 1IJK, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ijka_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1ijkb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1ijkc_, region C [Jmol] [rasmolscript] [script source]
  • Fold representative 1ijk 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: [1ijk_B] [1ijk] [1ijk_C] [1ijk_A]
  • SWISS-PROT database: [P22029] [P22030] [P04275]
  • Domain organization of [BOTA_BOTJA] [BOTB_BOTJA] [VWF_HUMAN] by SWISSPFAM
  • Domains found in 1IJK: [CLECT] [VWA ] by SMART
  • Alignments of the sequence of 1IJK with the sequences similar proteins can be viewed for 1IJK's classification [BOTA_BOTJA] [BOTB_BOTJA] [VWF_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [BOTA_BOTJA] [BOTB_BOTJA] [VWF_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1IJK
  • Community annotation for 1IJK 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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