3VN4 Hydrolase date Dec 21, 2011
title Crystal Structure Of The Exosite-Containing Fragment Of Huma (P475s Mutant)
authors D.Nakayama, M.Akiyama, S.Takeda, K.Kokame, J.Takagi, T.Miyata
compound source
Molecule: A Disintegrin And Metalloproteinase With Thrombos Motifs 13;
Chain: A
Fragment: Dtcs Domains, Unp Residues 287-685
Synonym: Adam-Ts 13, Adam-Ts13, Adamts-13, Von Willebrand F Cleaving Protease, Vwf-Cp, Vwf-Cleaving Protease;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Adamts13
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell_line: Hek293s Gnt1-
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcm-Nidsp
symmetry Space Group: C 1 2 1
R_factor 0.229 R_Free 0.277
length a length b length c angle alpha angle beta angle gamma
153.378 53.243 76.615 90.00 111.56 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand BGC, BMA, FUC, NAG enzyme Hydrolase E.C. BRENDA

Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (133 Kb) [Save to disk]
  • Biological Unit Coordinates (3vn4.pdb1.gz) 127 Kb
  • Biological Unit Coordinates (3vn4.pdb2.gz) 251 Kb
  • LPC: Ligand-Protein Contacts for 3VN4
  • CSU: Contacts of Structural Units for 3VN4
  • Structure Factors (216 Kb)
  • Retrieve 3VN4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VN4 from S2C, [Save to disk]
  • Re-refined 3vn4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3VN4 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 3VN4
  • 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 3VN4, from MSDmotif at EBI
  • Fold representative 3vn4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3vn4] [3vn4_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3VN4: [ACR] [TSP1 ] by SMART
  • Other resources with information on 3VN4
  • Community annotation for 3VN4 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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