4Y40 Hydrloase Inhibitor date Feb 10, 2015
title Structure Of Vaspin Mutant D305c V383c
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
Expression_system_taxid: 511693
symmetry Space Group: C 1 2 1
R_factor 0.180 R_Free 0.206
length a length b length c angle alpha angle beta angle gamma
133.495 152.340 61.611 90.00 97.05 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] (266 Kb) [Save to disk]
  • Biological Unit Coordinates (4y40.pdb1.gz) 133 Kb
  • Biological Unit Coordinates (4y40.pdb2.gz) 129 Kb
  • LPC: Ligand-Protein Contacts for 4Y40
  • CSU: Contacts of Structural Units for 4Y40
  • Structure Factors (3309 Kb)
  • Retrieve 4Y40 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4Y40 from S2C, [Save to disk]
  • Re-refined 4y40 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4Y40 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.
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  • Visual 3D analysis of 4Y40
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 4y40 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4y40_A] [4y40_B] [4y40]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4Y40: [SERPIN ] by SMART
  • Other resources with information on 4Y40
  • Community annotation for 4Y40 at PDBWiki (http://pdbwiki.org)

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