3D5M	Transferase	date	May 16, 2008
title	Crystal Structure Of Hcv Ns5b Polymerase With A Novel Pyrida Inhibitor
authors	Q.Zhao, R.E.Showalter, Q.Han, C.R.Kissinger
compound		source
Molecule: Rna-Directed Rna Polymerase Chain: A, B Fragment: Catalytic Domain (Residues 2420-2989) Synonym: Ns5b, P68 Ec: 2.7.7.48 Engineered: Yes Mutation: Yes		Organism_scientific: Hepatitis C Virus (Isolate Bk) Organism_taxid: 11105 Strain: Genotype 1b Bk Expression_system: Escherichia Coli Expression_system_strain: Bl21(De3)Star Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet21a
symmetry	Space Group: P 21 21 21	R_factor 0.208 R_Free 0.261
crystal cell	length a length b length c angle alpha angle beta angle gamma 86.304 106.765 126.254 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.20 Å
ligand	4MS BindingDB	enzyme	Transferase E.C.2.7.7.48 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Structure-based design, synthesis, and biological evaluation of 1,1-dioxoisothiazole and benzo[b]thiophene-1,1-dioxide derivatives as novel inhibitors of hepatitis C virus NS5B polymerase., Kim SH, Tran MT, Ruebsam F, Xiang AX, Ayida B, McGuire H, Ellis D, Blazel J, Tran CV, Murphy DE, Webber SE, Zhou Y, Shah AM, Tsan M, Showalter RE, Patel R, Gobbi A, LeBrun LA, Bartkowski DM, Nolan TG, Norris DA, Sergeeva MV, Kirkovsky L, Zhao Q, Han Q, Kissinger CR, Bioorg Med Chem Lett. 2008 Jul 15;18(14):4181-5. Epub 2008 May 24. PMID:18554907

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (187 Kb) [Save to disk] Biological Unit Coordinates (3d5m.pdb1.gz) 91 Kb Biological Unit Coordinates (3d5m.pdb2.gz) 91 Kb LPC: Ligand-Protein Contacts for 3D5M CSU: Contacts of Structural Units for 3D5M Likely Quarternary Molecular Structure file(s) for 3D5M Structure Factors (881 Kb) Retrieve 3D5M in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3D5M from S2C, [Save to disk] Re-refined 3d5m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3D5M 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 3D5M

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 3D5M, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3d5m_B] [3d5m_A] [3d5m] SWISS-PROT database: [P26663] Domain organization of [POLG_HCVBK] by SWISSPFAM

Other resources with information on 3D5M

Community annotation for 3D5M at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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