5KNN Ligase date Jun 28, 2016
title Evolutionary Gain Of Alanine Mischarging To Non-Cognate Trna G4:U69 Base Pair
authors L.Sun, W.He, X.L.Yang
compound source
Molecule: Alanine--Trna Ligase, Cytoplasmic
Chain: A, B, C, D, E, F, G, H
Fragment: Residues 4-453
Synonym: Alanyl-Trna Synthetase,Alars,Renal Carcinoma Antig 42;
Ec: 6.1.1.7
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Aars
Expression_system: Escherichia Coli-Pichia Pastoris Shuttle Ppparg4;
Expression_system_taxid: 1182032
symmetry Space Group: P 1
R_factor 0.216 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.167 98.260 201.385 90.07 89.95 90.11
method X-Ray Diffractionresolution 2.68 Å
ligand A5A enzyme Ligase E.C.6.1.1.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B, H, C, D, G


Primary referenceEvolutionary gain of alanine mischarging to non-cognate tRNAs with a G4:U69 base pair., Sun L, Gomes AC, He W, Zhou H, Wang X, Pan DW, Schimmel P, Pan T, Yang XL, J Am Chem Soc. 2016 Sep 13. PMID:27622773
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (586 Kb) [Save to disk]
  • Biological Unit Coordinates (5knn.pdb1.gz) 79 Kb
  • Biological Unit Coordinates (5knn.pdb2.gz) 79 Kb
  • Biological Unit Coordinates (5knn.pdb3.gz) 79 Kb
  • Biological Unit Coordinates (5knn.pdb4.gz) 79 Kb
  • Biological Unit Coordinates (5knn.pdb5.gz) 80 Kb
  • Biological Unit Coordinates (5knn.pdb6.gz) 79 Kb
  • Biological Unit Coordinates (5knn.pdb7.gz) 79 Kb
  • Biological Unit Coordinates (5knn.pdb8.gz) 79 Kb
  • LPC: Ligand-Protein Contacts for 5KNN
  • CSU: Contacts of Structural Units for 5KNN
  • Structure Factors (2395 Kb)
  • Retrieve 5KNN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5KNN from S2C, [Save to disk]
  • Re-refined 5knn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5KNN 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 5KNN
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5knn from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5knn_D] [5knn] [5knn_B] [5knn_C] [5knn_H] [5knn_E] [5knn_A] [5knn_F] [5knn_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5KNN
  • Community annotation for 5KNN at PDBWiki (http://pdbwiki.org)

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