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
  • Domain found in 3VN4: [TSP1 ] by SMART
  • Alignments of the sequence of 3VN4 with the sequences similar proteins can be viewed for 3VN4's classification 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 at ProtoMap. Click on the Cluster number.
  • 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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