6D06 Hydrolase Rna date Apr 10, 2018
title Human Adar2d E488y Mutant Complexed With Dsrna Containing An Site Opposite The Edited Base
authors M.M.Matthews, A.J.Fisher, P.A.Beal
compound source
Molecule: Double-Stranded Rna-Specific Editase 1
Chain: A, D
Synonym: Rna-Editing Deaminase 1,Rna-Editing Enzyme 1,Dsrna Deaminase;
Ec: 3.5.4.37
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Adarb1, Adar2, Drada2, Red1
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932
Expression_system_strain: Bcy123
Expression_system_vector_type: Vector
Expression_system_plasmid: Psc

Molecule: Rna (5'-R(Gpcpupcpgpcpgpapupgpcpup(8 Pgpapgpgpgpcpupcpupg)-3');
Chain: B
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Rna (5'- R(Cpapgpapgpcpcpcpcpcpnpapgpcpapupcpgpcp C)-3');
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: C 1 2 1
R_factor 0.190 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
174.680 63.440 132.060 90.00 126.64 90.00
method X-Ray Diffractionresolution 2.55 Å
ligand
enzyme Hydrolase E.C.3.5.4.37 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D


Primary referenceA Bump-Hole Approach for Directed RNA Editing., Monteleone LR, Matthews MM, Palumbo CM, Thomas JM, Zheng Y, Chiang Y, Fisher AJ, Beal PA, Cell Chem Biol. 2018 Nov 23. pii: S2451-9456(18)30385-4. doi:, 10.1016/j.chembiol.2018.10.025. PMID:30581135
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (147 Kb) [Save to disk]
  • Biological Unit Coordinates (6d06.pdb1.gz) 84 Kb
  • Biological Unit Coordinates (6d06.pdb2.gz) 59 Kb
  • CSU: Contacts of Structural Units for 6D06
  • Structure Factors (627 Kb)
  • Retrieve 6D06 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6D06 from S2C, [Save to disk]
  • View 6D06 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 6D06
  • 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 6d06 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6d06_B] [6d06_D] [6d06_C] [6d06_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6D06
  • Community annotation for 6D06 at PDBWiki (http://pdbwiki.org)

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