5HP3 Hydrolase Rna date Jan 20, 2016
title Human Adenosine Deaminase Acting On Dsrna (Adar2) Bound To D Sequence Derived From S. Cerevisiae Bdf2 Gene With Ac Misma Reaction Site
authors M.M.Matthews, A.J.Fisher, P.A.Beal
compound source
Molecule: Double-Stranded Rna-Specific Editase 1
Chain: A, D
Fragment: Unp Residues 299-701
Synonym: Rna-Editing Deaminase 1, Rna-Editing Enzyme 1, Dsr Adenosine Deaminase;
Ec: 3.5.4.37
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Adarb1, 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 0.238
crystal
cell
length a length b length c angle alpha angle beta angle gamma
81.510 107.210 120.620 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.09 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] (314 Kb) [Save to disk]
  • Biological Unit Coordinates (5hp3.pdb1.gz) 174 Kb
  • Biological Unit Coordinates (5hp3.pdb2.gz) 134 Kb
  • LPC: Ligand-Protein Contacts for 5HP3
  • CSU: Contacts of Structural Units for 5HP3
  • Structure Factors (368 Kb)
  • Retrieve 5HP3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5HP3 from S2C, [Save to disk]
  • Re-refined 5hp3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5HP3 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 5HP3
  • 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 5hp3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5hp3_C] [5hp3_D] [5hp3_A] [5hp3] [5hp3_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5HP3: [ADEAMc ] by SMART
  • Other resources with information on 5HP3
  • Community annotation for 5HP3 at PDBWiki (http://pdbwiki.org)

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