5CCB Transferase Rna date Jul 01, 2015
title Crystal Structure Of Human M1a58 Methyltransferase In A Comp Trna3lys And Sah
authors J.Finer-Moore, N.Czudnochowski, J.D.O'Connell Iii, A.L.Wang, R.M
compound source
Molecule: Trna (Adenine(58)-N(1))-Methyltransferase Catalyt Trmt61a;
Chain: A
Synonym: Trna(M1a58)-Methyltransferase Subunit Trmt61a,Trna Mtase Subunit Trmt61a;
Ec: 2.1.1.220
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Trmt61a, C14orf172, Trm61
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_cell_line: Bl21(De3)
Expression_system_plasmid: Pet17b-6histrm6-Trm61

Molecule: Trna (Adenine(58)-N(1))-Methyltransferase Non-Cat Subunit Trm6;
Chain: B
Synonym: Trna(M1a58)-Methyltransferase Subunit Trm6,Trna(M1 Subunit Trm6;
Ec: 2.1.1.220
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Trmt6, Kiaa1153, Trm6, Cgi-09
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_cell_line: Bl21(De3)
Expression_system_plasmid: Pet17b-6histrm6-Trm61

Molecule: Trna3lys
Chain: N
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 43 21 2
R_factor 0.199 R_Free 0.222
crystal
cell
length a length b length c angle alpha angle beta angle gamma
137.180 137.180 177.020 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand NA, SAH enzyme Transferase E.C.2.1.1.220 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceCrystal Structure of the Human tRNA m(1)A58 Methyltransferase-tRNA3(Lys) Complex: Refolding of Substrate tRNA Allows Access to the Methylation Target., Finer-Moore J, Czudnochowski N, O'Connell JD 3rd, Wang AL, Stroud RM, J Mol Biol. 2015 Dec 4;427(24):3862-76. doi: 10.1016/j.jmb.2015.10.005. Epub 2015, Oct 22. PMID:26470919
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (261 Kb) [Save to disk]
  • Biological Unit Coordinates (5ccb.pdb1.gz) 504 Kb
  • LPC: Ligand-Protein Contacts for 5CCB
  • CSU: Contacts of Structural Units for 5CCB
  • Structure Factors (2213 Kb)
  • Retrieve 5CCB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5CCB from S2C, [Save to disk]
  • Re-refined 5ccb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5CCB 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 5CCB
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ccb_B] [5ccb_A] [5ccb_N] [5ccb]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5CCB
  • Community annotation for 5CCB at PDBWiki (http://pdbwiki.org)

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