3KNX	Viral Protein	date	Nov 12, 2009
title	Hcv Ns3 Protease Domain With P1-P3 Macrocyclic Ketoamide Inh
authors	S.Venkatraman, F.Velazquez, W.Wu, M.Blackman, K.X.Chen, S.Bogen, L X.Tong, R.Chase, A.Hart, S.Agrawal, J.Pichardo, A.Prongay, K.C.C V.Girijavallabhan, J.Piwinski, N.Y.Shih, F.G.Njoroge
compound		source
Molecule: Hcv Ns3 Protease Chain: A, C Fragment: Protease Domain, Unp Residues 1027-1207 Engineered: Yes		Organism_scientific: Hepatitis C Virus Subtype 1a Organism_taxid: 63746 Strain: H77 Strain Of Genotype 1a Gene: Ns3 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Pet-3a
Molecule: Hcv Ns4a Peptide Chain: B, D Fragment: Unp Residues 1678-1696 Engineered: Yes Mutation: Yes		Synthetic: Yes Other_details: Peptides Were Synthesized Using Fmoc Solid-P Chemistry On An Abi 431 Synthesizer (Foster City, Ca). Prel Chlorotrityl Chloride Resin Or Wang Resin Was Used For The Phase Assembly Of Ns4a Activator Peptide. The Sequence Of T Peptide Was Lys-Lys-Gly-Ser-Val-Val-Ile-Val-Gly-Arg-Ile-Ile Gly-Arg-Pro-Ala-Ile-Val-Pro-Lys-Lys-Oh. Trifunctional Resid Sidechain Protecting Groups Included Tert-Butyl For Ser, Te Butoxycarbonyl For Lys, And 2,2,4,6,7-Pentamethyldihydroben 5-Sulfonyl For Arg. Cleavage And Sidechain Deprotection Was Accomplished Using 92.5% Trifluoroacetic Acid, With 2.5% Ea Water, Ethanedithiol And Triisopropylsilane For 2 Hours. Th Was Purified By Reversed Phase Hplc. The Peptide Molecular Was Confirmed By Electrospray Ionization Mass Spectrometry.
symmetry	Space Group: H 3 2	R_factor 0.169 R_Free 0.263
crystal cell	length a length b length c angle alpha angle beta angle gamma 223.587 223.587 75.282 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.65 Å
ligand	BME, JZT, ZN	enzyme
Gene Ontology	Chain Function Process Component A, C D, B
Primary reference	Discovery and structure-activity relationship of P1-P3 ketoamide derived macrocyclic inhibitors of hepatitis C virus NS3 protease., Venkatraman S, Velazquez F, Wu W, Blackman M, Chen KX, Bogen S, Nair L, Tong X, Chase R, Hart A, Agrawal S, Pichardo J, Prongay A, Cheng KC, Girijavallabhan V, Piwinski J, Shih NY, Njoroge FG, J Med Chem. 2009 Jan 22;52(2):336-46. PMID:19102654

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (67 Kb) [Save to disk] Biological Unit Coordinates (3knx.pdb1.gz) 35 Kb Biological Unit Coordinates (3knx.pdb2.gz) 28 Kb LPC: Ligand-Protein Contacts for 3KNX CSU: Contacts of Structural Units for 3KNX Structure Factors (143 Kb) Retrieve 3KNX in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3KNX from S2C, [Save to disk] Re-refined 3knx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3KNX 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 3KNX

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 3KNX, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3knx] [3knx_D] [3knx_A] [3knx_B] [3knx_C] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 3KNX

Community annotation for 3KNX at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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