2Q6F Hydrolase date Jun 05, 2007
title Crystal Structure Of Infectious Bronchitis Virus (Ibv) Main In Complex With A Michael Acceptor Inhibitor N3
authors X.Y.Xue, H.T.Yang, F.Xue, M.Bartlam, Z.H.Rao
compound source
Molecule: Infectious Bronchitis Virus (Ibv) Main Protease
Chain: A, B
Synonym: Fragment
Ec: 3.4.22.-
Engineered: Yes
Organism_scientific: Infectious Bronchitis Virus
Organism_taxid: 11120
Strain: M41
Gene: M41 3c-Like Protease Gene
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-4t-1

Molecule: N-[(5-Methylisoxazol-3-Yl)Carbonyl]Alanyl-L-Valyl ((1r,2z)-4-(Benzyloxy)-4-Oxo-1-{[(3r)-2-Oxopyrrolidin-3- Yl]Methyl}But-2-Enyl)-L-Leucinamide;
Chain: D, C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1
R_factor 0.216 R_Free 0.242
crystal
cell
length a length b length c angle alpha angle beta angle gamma
53.175 54.502 66.719 111.06 104.31 91.33
method X-Ray Diffractionresolution 2.00 Å
ligand 010, 02J, PJE enzyme Hydrolase E.C.3.4.22 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructures of two coronavirus main proteases: implications for substrate binding and antiviral drug design., Xue X, Yu H, Yang H, Xue F, Wu Z, Shen W, Li J, Zhou Z, Ding Y, Zhao Q, Zhang XC, Liao M, Bartlam M, Rao Z, J Virol. 2008 Mar;82(5):2515-27. Epub 2007 Dec 19. PMID:18094151
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (106 Kb) [Save to disk]
  • Biological Unit Coordinates (2q6f.pdb1.gz) 101 Kb
  • LPC: Ligand-Protein Contacts for 2Q6F
  • CSU: Contacts of Structural Units for 2Q6F
  • Likely Quarternary Molecular Structure file(s) for 2Q6F
  • Structure Factors (645 Kb)
  • Retrieve 2Q6F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2Q6F from S2C, [Save to disk]
  • Re-refined 2q6f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2Q6F 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 2Q6F
  • 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
  • 3D motif for 2Q6F, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2q6f] [2q6f_A] [2q6f_C] [2q6f_B] [2q6f_D]
  • SWISS-PROT database: [P0C6Y3]
  • Domain organization of [R1AB_IBVM] by SWISSPFAM
  • Other resources with information on 2Q6F
  • Community annotation for 2Q6F at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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