1V7P Toxin Cell Adhesion date Dec 19, 2003
title Structure Of Ems16-Alpha2-I Domain Complex
authors K.Horii, D.Okuda, T.Morita, H.Mizuno
compound source
Molecule: Ems16 A Chain
Chain: A
Fragment: Residues 1-134
Synonym: Ems16 Subunit A
Organism_scientific: Echis Multisquamatus
Organism_taxid: 93050

Molecule: Ems16 B Chain
Chain: B
Fragment: Residues 1-128
Synonym: Ems16 Subunit B
Mutation: Yes

Organism_scientific: Echis Multisquamatus
Organism_taxid: 93050

Molecule: Integrin Alpha-2
Chain: C
Fragment: Residues 138-337
Synonym: Alpha2-I, Platelet Membrane Glycoprotein Ia, Gpia, Receptor, Vla-2 Alpha Chain, Cd49b;
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plamid
Expression_system_plasmid: Pet32a
symmetry Space Group: C 1 2 1
R_factor 0.188 R_Free 0.235
length a length b length c angle alpha angle beta angle gamma
163.766 38.449 69.524 90.00 91.52 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand CL, MN, NAG, PO4 enzyme
note 1V7P (Molecule of the Month:pdb134)is a representative structure
related structures by homologous chain: 1DZI, 1UKM
A, B
  • toxin activity

  • Primary referenceCrystal structure of EMS16 in complex with the integrin alpha2-I domain., Horii K, Okuda D, Morita T, Mizuno H, J Mol Biol 2004 Aug 6;341(2):519-27. PMID:15276841
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (89 Kb) [Save to disk]
  • Biological Unit Coordinates (1v7p.pdb1.gz) 83 Kb
  • LPC: Ligand-Protein Contacts for 1V7P
  • CSU: Contacts of Structural Units for 1V7P
  • Likely Quarternary Molecular Structure file(s) for 1V7P
  • Structure Factors (278 Kb)
  • Retrieve 1V7P in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1V7P from S2C, [Save to disk]
  • Re-refined 1v7p structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1V7P 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 1V7P
  • 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 1V7P, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1v7pa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1v7pb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1v7pc_, region C [Jmol] [rasmolscript] [script source]
  • 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: [1v7p_C] [1v7p_A] [1v7p_B] [1v7p]
  • SWISS-PROT database: [Q7T2Q1] [Q7T2Q0] [P17301]
  • Domain organization of [EM16A_ECHML] [EM16B_ECHML] [ITA2_HUMAN] by SWISSPFAM
  • Domains found in 1V7P: [CLECT] [VWA ] by SMART
  • Other resources with information on 1V7P
  • Community annotation for 1V7P 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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