4PYW Hydrolase Inhibitor date Mar 28, 2014
title 1.92 Angstrom Crystal Structure Of A1at:Ttai Ternary Complex
authors M.P.Nyon, J.Day, B.Gooptu
compound source
Molecule: Alpha-1-Antitrypsin
Chain: A
Synonym: Alpha-1 Protease Inhibitor, Alpha-1-Antiproteinase A1, Short Peptide From Aat, Spaat;
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Serpina1, Aat, Pi, Pro0684, Pro2209
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Xl1 Blue
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pqe32b

Molecule: Ace-Thr-Thr-Ala-Ile-Nh2
Chain: B, C
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: C 1 2 1
R_factor 0.190 R_Free 0.225
crystal
cell
length a length b length c angle alpha angle beta angle gamma
113.710 38.960 93.130 90.00 100.13 90.00
method X-Ray Diffractionresolution 1.91 Å
ligand ACE, GOL, NH2 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A
  • COPII vesicle coating

    • Primary referenceAn integrative approach combining ion mobility mass spectrometry, X-ray crystallography and NMR spectroscopy to study the conformational dynamics of alpha -antitrypsin upon ligand binding., Nyon MP, Prentice T, Day J, Kirkpatrick J, Sivalingam GN, Levy G, Haq I, Irving JA, Lomas DA, Christodoulou J, Gooptu B, Thalassinos K, Protein Sci. 2015 May 26. doi: 10.1002/pro.2706. PMID:26011795
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (134 Kb) [Save to disk]
  • Biological Unit Coordinates (4pyw.pdb1.gz) 127 Kb
  • LPC: Ligand-Protein Contacts for 4PYW
  • CSU: Contacts of Structural Units for 4PYW
  • Structure Factors (970 Kb)
  • Retrieve 4PYW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4PYW from S2C, [Save to disk]
  • Re-refined 4pyw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4PYW 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 4PYW
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4PYW, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4pyw_C] [4pyw_A] [4pyw_B] [4pyw]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4PYW: [SERPIN ] by SMART
    • Other resources with information on 4PYW
  • Community annotation for 4PYW at PDBWiki (http://pdbwiki.org)

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