5ED2 Hydrolase Rna date Oct 20, 2015
title Human Adenosine Deaminase Acting On Dsrna (Adar2) Mutant E48 To Dsrna Sequence Derived From Human Gli1 Gene
authors M.M.Matthews, A.J.Fisher
compound source
Molecule: Double-Stranded Rna-Specific Editase 1
Chain: A, D
Fragment: A To I Editase (Unp Residues 327-729)
Synonym: Adenosine Deaminase Acting On Rna
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Adar2, Drada2, Red1
Expression_system: Saccharomyces Cerevisiae
Expression_system_common: Yeast
Expression_system_taxid: 4932
Expression_system_strain: Bcy123
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Psc

Molecule: Rna (5'-R(Pgpcpupcpgpcpgpapupgpcpup( Pgpapgpgpgpcpupcpupg)-3');
Chain: B, E
Engineered: Yes

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

Molecule: Rna (5'- R(Pcpapgpapgpcpcpcpcpcpcpapgpcpapupcpgpc C)-3');
Chain: C, F
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 21 21 21
R_factor 0.188 R_Free 0.208
length a length b length c angle alpha angle beta angle gamma
79.130 81.614 256.618 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.95 Å
ligand 8AZ, IHP, ZN enzyme Hydrolase E.C. BRENDA
A, D

Primary referenceStructures of human ADAR2 bound to dsRNA reveal base-flipping mechanism and basis for site selectivity., Matthews MM, Thomas JM, Zheng Y, Tran K, Phelps KJ, Scott AI, Havel J, Fisher AJ, Beal PA, Nat Struct Mol Biol. 2016 May;23(5):426-33. doi: 10.1038/nsmb.3203. Epub 2016 Apr, 11. PMID:27065196
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (359 Kb) [Save to disk]
  • Biological Unit Coordinates (5ed2.pdb1.gz) 175 Kb
  • Biological Unit Coordinates (5ed2.pdb2.gz) 175 Kb
  • LPC: Ligand-Protein Contacts for 5ED2
  • CSU: Contacts of Structural Units for 5ED2
  • Structure Factors (2230 Kb)
  • Retrieve 5ED2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5ED2 from S2C, [Save to disk]
  • Re-refined 5ed2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5ED2 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 5ED2
  • 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
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1w5ed2, region D:232-354 [Jmol] [rasmolscript] [script source]
        - Domain d1p5ed2, region D:310-432 [Jmol] [rasmolscript] [script source]
  • Fold representative 5ed2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ed2_E] [5ed2] [5ed2_F] [5ed2_C] [5ed2_B] [5ed2_A] [5ed2_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5ED2: [ADEAMc ] by SMART
  • Other resources with information on 5ED2
  • Community annotation for 5ED2 at PDBWiki (http://pdbwiki.org)

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