1WK9	Ligase	date	May 30, 2004
title	Structural Basis For Non-Cognate Amino Acid Discrimination B Valyl-Trna Synthetase Editing Domain
authors	R.Fukunaga, S.Yokoyama, Riken Structural Genomicsproteomics I (Rsgi)
compound		source
Molecule: Valyl-Trna Synthetase Chain: A Fragment: Cp1 Domain Synonym: Valine--Trna Ligase, Valrs Ec: 6.1.1.9 Engineered: Yes		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet26b
symmetry	Space Group: P 65 2 2	R_factor 0.205 R_Free 0.247
crystal cell	length a length b length c angle alpha angle beta angle gamma 95.490 95.490 72.300 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	1.75 Å
ligand	TSB	enzyme	Ligase E.C.6.1.1.9 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain., Fukunaga R, Yokoyama S, J Biol Chem 2005 Aug 19;280(33):29937-45. Epub 2005 Jun 21. PMID:15970591

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (32 Kb) [Save to disk] Biological Unit Coordinates (1wk9.pdb1.gz) 28 Kb LPC: Ligand-Protein Contacts for 1WK9 CSU: Contacts of Structural Units for 1WK9 Likely Quarternary Molecular Structure file(s) for 1WK9 Structure Factors (182 Kb) Retrieve 1WK9 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1WK9 from S2C, [Save to disk] Re-refined 1wk9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1WK9 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 1WK9

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 1WK9, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1wk9_A] [1wk9] SWISS-PROT database: [P96142] Domain organization of [SYV_THETH] by SWISSPFAM

Other resources with information on 1WK9

Community annotation for 1WK9 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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