5ED1 Hydrolase Rna date Oct 20, 2015
title Human Adenosine Deaminase Acting On Dsrna (Adar2) Mutant E48 To Dsrna Sequence Derived From S. Cerevisiae Bdf2 Gene
authors M.M.Matthews, A.J.Fisher, P.A.Beal
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
Ec: 3.5.4.37
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(Upupcpcpcpcpapcpapupup(8az) Pgpapcpgpupupcpapgpupc)-3');
Chain: B
Engineered: Yes

Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932

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

Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
symmetry Space Group: P 21 21 21
R_factor 0.163 R_Free 0.223
crystal
cell
length a length b length c angle alpha angle beta angle gamma
82.362 107.498 121.097 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.77 Å
ligand 8AZ, IHP, ZN enzyme Hydrolase E.C.3.5.4.37 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
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] (320 Kb) [Save to disk]
  • Biological Unit Coordinates (5ed1.pdb1.gz) 177 Kb
  • Biological Unit Coordinates (5ed1.pdb2.gz) 136 Kb
  • LPC: Ligand-Protein Contacts for 5ED1
  • CSU: Contacts of Structural Units for 5ED1
  • Structure Factors (1633 Kb)
  • Retrieve 5ED1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5ED1 from S2C, [Save to disk]
  • Re-refined 5ed1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5ED1 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 5ED1
  • 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 d1p5ed1, region D:175-309 [Jmol] [rasmolscript] [script source]
        - Domain d1w5ed1, region D:23-231 [Jmol] [rasmolscript] [script source]
  • Fold representative 5ed1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ed1_C] [5ed1] [5ed1_D] [5ed1_A] [5ed1_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5ED1: [ADEAMc ] by SMART
  • Other resources with information on 5ED1
  • Community annotation for 5ED1 at PDBWiki (http://pdbwiki.org)

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