1GAX	Ligase Rna	date	Jun 23, 2000
title	Crystal Structure Of Thermus Thermophilus Valyl-Trna Synthet Complexed With Trna(Val) And Valyl-Adenylate Analogue
authors	S.Fukai, O.Nureki, S.Sekine, A.Shimada, J.Tao, D.G.Vassylyev, S.Yo Riken Structural Genomicsproteomics Initiative (Rsgi)
compound		source
Molecule: Trna(Val) Chain: C, D Engineered: Yes		Synthetic: Yes Other_details: Sequence From Thermus Thermophilus
Molecule: Valyl-Trna Synthetase Chain: A, B Synonym: Valrs Ec: 6.1.1.9 Engineered: Yes		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pk7
symmetry	Space Group: P 42 21 2	R_factor 0.245 R_Free 0.272
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, ZN	enzyme	Ligase E.C.6.1.1.9 BRENDA
note	1GAX (Molecule of the Month:pdb16)
related structures	by homologous chain: 1IVS
Gene Ontology	Chain Function Process Component A, B aminoacyl-tRNA editing activ...
Primary reference	Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA synthetase., Fukai S, Nureki O, Sekine S, Shimada A, Tao J, Vassylyev DG, Yokoyama S, Cell 2000 Nov 22;103(5):793-803. PMID:11114335

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (351 Kb) [Save to disk] Biological Unit Coordinates (1gax.pdb1.gz) 175 Kb Biological Unit Coordinates (1gax.pdb2.gz) 175 Kb LPC: Ligand-Protein Contacts for 1GAX CSU: Contacts of Structural Units for 1GAX Likely Quarternary Molecular Structure file(s) for 1GAX Retrieve 1GAX in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1GAX from S2C, [Save to disk]

View 1GAX 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 1GAX

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1GAX, from MSDmotif at EBI Structure summary from SCOR (Structural Classification of RNA) Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1gaxa3, region A:1-189,A:343-578 [Jmol] [rasmolscript] [script source]     - Domain d1gaxa2, region A:190-342 [Jmol] [rasmolscript] [script source]     - Domain d1gaxa5, region A:579-796 [Jmol] [rasmolscript] [script source]     - Domain d1gaxa4, region A:797-862 [Jmol] [rasmolscript] [script source]     - Domain d1gaxb3, region B:1-189,B:343-578 [Jmol] [rasmolscript] [script source]     - Domain d1gaxb2, region B:190-342 [Jmol] [rasmolscript] [script source]     - Domain d1gaxb5, region B:579-796 [Jmol] [rasmolscript] [script source]     - Domain d1gaxb4, 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: [1gax_B] [1gax_D] [1gax_C] [1gax] [1gax_A] SWISS-PROT database: [P96142] Domain organization of [SYV_THETH] by SWISSPFAM

Other resources with information on 1GAX

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

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