4Y3K Hydrolase Inhibitor date Feb 10, 2015
title Structure Of Vaspin Mutant E379s
authors J.Pippel, N.Strater, D.Ulbricht, S.Schultz, R.Meier, J.T.Heiker
compound source
Molecule: Serpin A12
Chain: A, B
Fragment: Unp Residues 22-414
Synonym: Ol-64,Visceral Adipose Tissue-Derived Serine Prote Inhibitor,Vaspin,Visceral Adipose-Specific Serpin;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Serpina12
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
symmetry Space Group: C 1 2 1
R_factor 0.186 R_Free 0.219
length a length b length c angle alpha angle beta angle gamma
132.959 151.353 61.602 90.00 98.43 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand EDO, SO4 enzyme
A, B

Primary referenceA unique serpin P1' glutamate and a conserved beta-sheet C arginine are key residues for activity, protease recognition and stability of serpinA12 (vaspin)., Ulbricht D, Pippel J, Schultz S, Meier R, Strater N, Heiker JT, Biochem J. 2015 Jul 21. pii: BJ20150643. PMID:26199422
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (268 Kb) [Save to disk]
  • Biological Unit Coordinates (4y3k.pdb1.gz) 133 Kb
  • Biological Unit Coordinates (4y3k.pdb2.gz) 132 Kb
  • LPC: Ligand-Protein Contacts for 4Y3K
  • CSU: Contacts of Structural Units for 4Y3K
  • Structure Factors (3275 Kb)
  • Retrieve 4Y3K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4Y3K from S2C, [Save to disk]
  • Re-refined 4y3k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4Y3K 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 4Y3K
  • 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
  • Fold representative 4y3k from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4y3k_A] [4y3k_B] [4y3k]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4Y3K: [SERPIN ] by SMART
  • Other resources with information on 4Y3K
  • Community annotation for 4Y3K at PDBWiki (http://pdbwiki.org)

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