5C7B Apoptosis date Jun 24, 2015
title Fragment-Based Drug Discovery Targeting Inhibitor Of Apoptos Proteins: Compound 5
authors G.Chessari, I.M.Buck, J.E.H.Day, P.J.Day, A.Iqbal, C.N.Johnson, E. V.Martins, D.Miller, M.Reader, D.C.Rees, S.J.Rich, E.Tamanini, M. G.A.Ward, P.A.Williams, G.Williams, N.E.Wilsher, A.J.A.Woolfor
compound source
Molecule: E3 Ubiquitin-Protein Ligase Xiap
Chain: A
Fragment: Unp Residues 249-354
Synonym: Baculoviral Iap Repeat-Containing Protein 4,Iap-Li Protein,Hilp,Inhibitor Of Apoptosis Protein 3,Hiap3,X-Linke Inhibitor Of Apoptosis Protein,X-Linked Iap;
Ec: 6.3.2.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Xiap, Api3, Birc4, Iap3
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet 28b
symmetry Space Group: P 41 2 2
R_factor 0.202 R_Free 0.265
crystal
cell
length a length b length c angle alpha angle beta angle gamma
71.153 71.153 105.386 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.68 Å
ligand 4YD, ZN enzyme Ligase E.C.6.3.2 BRENDA
Primary referenceFragment-Based Drug Discovery Targeting Inhibitor of Apoptosis Proteins: Discovery of a Non-Alanine Lead Series with Dual Activity Against cIAP1 and XIAP., Chessari G, Buck IM, Day JE, Day PJ, Iqbal A, Johnson CN, Lewis EJ, Martins V, Miller D, Reader M, Rees DC, Rich SJ, Tamanini E, Vitorino M, Ward GA, Williams PA, Williams G, Wilsher NE, Woolford AJ, J Med Chem. 2015 Aug 7. PMID:26218264
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (45 Kb) [Save to disk]
  • Biological Unit Coordinates (5c7b.pdb1.gz) 40 Kb
  • LPC: Ligand-Protein Contacts for 5C7B
  • CSU: Contacts of Structural Units for 5C7B
  • Structure Factors (143 Kb)
  • Retrieve 5C7B in mmCIF format [Save to disk]
  • Re-refined 5c7b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5C7B 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 5C7B
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5c7b_A] [5c7b]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5C7B: [BIR ] by SMART
  • Other resources with information on 5C7B
  • Community annotation for 5C7B at PDBWiki (http://pdbwiki.org)

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