3VYY Hydrolase Rna date Oct 05, 2012
title Structural Insights Into Risc Assembly Facilitated By Dsrna Domains Of Human Rna Helicase A (Dhx9)
authors Y.A.Yuan, Q.Fu
compound source
Molecule: Atp-Dependent Rna Helicase A
Chain: A, B
Fragment: Unp Residues 1-91
Synonym: Rha, Deah Box Protein 9, Leukophysin, Lkp, Nuclear Helicase II, Ndh II;
Ec: 3.6.4.13
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dhx9, Ddx9, Lkp, Ndh2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid

Molecule: Rna (5'-R(Gpcpgpcpgpcpgpcpgpc)-3')
Chain: C, D, E, F, G
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: The Sequence Is Synthesized In Vitro.
symmetry Space Group: C 1 2 1
R_factor 0.219 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.252 78.529 112.242 90.00 98.81 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand
enzyme Hydrolase E.C.3.6.4.13 BRENDA
Primary referenceStructural insights into RISC assembly facilitated by dsRNA-binding domains of human RNA helicase A (DHX9)., Fu Q, Yuan YA, Nucleic Acids Res. 2013 Jan 29. PMID:23361462
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (107 Kb) [Save to disk]
  • Biological Unit Coordinates (3vyy.pdb1.gz) 47 Kb
  • Biological Unit Coordinates (3vyy.pdb2.gz) 47 Kb
  • Biological Unit Coordinates (3vyy.pdb3.gz) 19 Kb
  • CSU: Contacts of Structural Units for 3VYY
  • Structure Factors (146 Kb)
  • Retrieve 3VYY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VYY from S2C, [Save to disk]
  • Re-refined 3vyy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3VYY 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 3VYY
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3VYY, from MSDmotif at EBI
  • Fold representative 3vyy from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3vyy_F] [3vyy_A] [3vyy_D] [3vyy_C] [3vyy_G] [3vyy_B] [3vyy] [3vyy_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3VYY: [DSRM ] by SMART
  • Other resources with information on 3VYY
  • Community annotation for 3VYY at PDBWiki (http://pdbwiki.org)

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