1NYR	Ligase	date	Feb 13, 2003
title	Structure Of Staphylococcus Aureus Threonyl-Trna Synthetase With Atp
authors	A.Torres-Larios, R.Sankaranarayanan, B.Rees, A.C.Dock-Bregeon, D
compound		source
Molecule: Threonyl-Trna Synthetase 1 Chain: A, B Ec: 6.1.1.3 Engineered: Yes		Organism_scientific: Staphylococcus Aureus Organism_taxid: 1280 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21de3 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pblue-Pet
symmetry	Space Group: P 21 21 21	R_factor 0.239 R_Free 0.313
crystal cell	length a length b length c angle alpha angle beta angle gamma 104.130 122.521 148.661 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.80 Å
ligand	ATP, THR, ZN	enzyme	Ligase E.C.6.1.1.3 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Conformational movements and cooperativity upon amino acid, ATP and tRNA binding in threonyl-tRNA synthetase., Torres-Larios A, Sankaranarayanan R, Rees B, Dock-Bregeon AC, Moras D, J Mol Biol 2003 Aug 1;331(1):201-11. PMID:12875846

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (219 Kb) [Save to disk] Biological Unit Coordinates (1nyr.pdb1.gz) 212 Kb LPC: Ligand-Protein Contacts for 1NYR CSU: Contacts of Structural Units for 1NYR Likely Quarternary Molecular Structure file(s) for 1NYR Structure Factors (380 Kb) Retrieve 1NYR in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1NYR from S2C, [Save to disk] Re-refined 1nyr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1NYR 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 1NYR

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 1NYR, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1nyra4, region A:242-532 [Jmol] [rasmolscript] [script source]     - Domain d1nyra2, region A:4-62 [Jmol] [rasmolscript] [script source]     - Domain d1nyra1, region A:533-645 [Jmol] [rasmolscript] [script source]     - Domain d1nyra3, region A:63-241 [Jmol] [rasmolscript] [script source]     - Domain d1nyrb2, region B:1-62 [Jmol] [rasmolscript] [script source]     - Domain d1nyrb4, region B:242-532 [Jmol] [rasmolscript] [script source]     - Domain d1nyrb1, region B:533-645 [Jmol] [rasmolscript] [script source]     - Domain d1nyrb3, region B:63-241 [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1nyr_A] [1nyr] [1nyr_B] SWISS-PROT database: [Q8NW68] Domain organization of [SYT_STAAW] by SWISSPFAM Domain found in 1NYR: [tRNA_SAD ] by SMART

Other resources with information on 1NYR

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

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