1IVS	Ligase Rna	date	Mar 29, 2002
title	Crystal Structure Of Thermus Thermophilus Valyl-Trna Synthet Complexed With Trna(Val) And Valyl-Adenylate Analogue
authors	S.Fukai, O.Nureki, S.I.Sekine, A.Shimada, D.G.Vassylyev, S.Yokoy Structural Genomicsproteomics Initiative (Rsgi)
compound		source
Molecule: Trna (Val) Chain: C, D Engineered: Yes Other_details: Trna (Val) With The Cac Anticodon		Synthetic: Yes
Molecule: Valyl-Trna Synthetase Chain: A, B Synonym: Valine-Trna Ligase, Valrs Ec: 6.1.1.9 Engineered: Yes		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Gene: Vals Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Jm109(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pk7
symmetry	Space Group: P 42 21 2	R_factor 0.248 R_Free 0.282
crystal cell	length a length b length c angle alpha angle beta angle gamma 411.810 411.810 81.970 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.90 Å
ligand	VAA	enzyme	Ligase E.C.6.1.1.9 BRENDA
related structures	by homologous chain: 1GAX
Gene Ontology	Chain Function Process Component A, B aminoacyl-tRNA editing activ...
Primary reference	Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase., Fukai S, Nureki O, Sekine S, Shimada A, Vassylyev DG, Yokoyama S, RNA 2003 Jan;9(1):100-11. PMID:12554880

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (352 Kb) [Save to disk] Biological Unit Coordinates (1ivs.pdb1.gz) 176 Kb Biological Unit Coordinates (1ivs.pdb2.gz) 175 Kb LPC: Ligand-Protein Contacts for 1IVS CSU: Contacts of Structural Units for 1IVS Likely Quarternary Molecular Structure file(s) for 1IVS Retrieve 1IVS in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1IVS from S2C, [Save to disk]

View 1IVS 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 1IVS

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1IVS, from MSDmotif at EBI Structure summary from SCOR (Structural Classification of RNA) Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1ivsa4, region A:1-189,A:343-578 [Jmol] [rasmolscript] [script source]     - Domain d1ivsa3, region A:190-342 [Jmol] [rasmolscript] [script source]     - Domain d1ivsa2, region A:579-796 [Jmol] [rasmolscript] [script source]     - Domain d1ivsa1, region A:797-862 [Jmol] [rasmolscript] [script source]     - Domain d1ivsb4, region B:1-189,B:343-578 [Jmol] [rasmolscript] [script source]     - Domain d1ivsb3, region B:190-342 [Jmol] [rasmolscript] [script source]     - Domain d1ivsb2, region B:579-796 [Jmol] [rasmolscript] [script source]     - Domain d1ivsb1, region B:797-862 [Jmol] [rasmolscript] [script source] Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1ivs_C] [1ivs_A] [1ivs_D] [1ivs] [1ivs_B] SWISS-PROT database: [P96142] Domain organization of [SYV_THETH] by SWISSPFAM

Other resources with information on 1IVS

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

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