2D6F	Ligase Rna	date	Nov 13, 2005
title	Crystal Structure Of Glu-Trna(Gln) Amidotransferase In The C With Trna(Gln)
authors	O.Nureki
compound		source
Molecule: Trna Chain: E, F Engineered: Yes		Synthetic: Yes
Molecule: Glutamyl-Trna(Gln) Amidotransferase Subunit D Chain: A, B Synonym: Gatd, Glu-Adt Subunit D Ec: 6.3.5.- Engineered: Yes		Organism_scientific: Methanothermobacter Thermautotrophicus Organism_taxid: 145262 Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Glutamyl-Trna(Gln) Amidotransferase Subunit E Chain: C, D Synonym: Gate, Glu-Adt Subunit E Ec: 6.3.5.- Engineered: Yes		Organism_scientific: Methanothermobacter Thermautotrophicus Organism_taxid: 145262 Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 21 21 21	R_factor 0.230 R_Free 0.292
crystal cell	length a length b length c angle alpha angle beta angle gamma 118.812 140.706 186.044 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.15 Å
ligand	ZN	enzyme	Ligase E.C.6.3.5 BRENDA
Gene Ontology	Chain Function Process Component A, B D, C
Primary reference	Structural basis of RNA-dependent recruitment of glutamine to the genetic code., Oshikane H, Sheppard K, Fukai S, Nakamura Y, Ishitani R, Numata T, Sherrer RL, Feng L, Schmitt E, Panvert M, Blanquet S, Mechulam Y, Soll D, Nureki O, Science. 2006 Jun 30;312(5782):1950-4. PMID:16809540

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (358 Kb) [Save to disk] Biological Unit Coordinates (2d6f.pdb1.gz) 351 Kb LPC: Ligand-Protein Contacts for 2D6F CSU: Contacts of Structural Units for 2D6F Likely Quarternary Molecular Structure file(s) for 2D6F Structure Factors (494 Kb) Retrieve 2D6F in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2D6F from S2C, [Save to disk] Re-refined 2d6f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2D6F 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 2D6F

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 2D6F, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2d6f_A] [2d6f_F] [2d6f_E] [2d6f_B] [2d6f_D] [2d6f_C] [2d6f] SWISS-PROT database: [O26802] [O26803] Domain organization of [GATD_METTH] [GATE_METTH] by SWISSPFAM Domains found in 2D6F: [Asparaginase] [GatB_Yqey ] by SMART

Other resources with information on 2D6F

Community annotation for 2D6F at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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