4NGF Hydrolase Rna date Nov 01, 2013
title Structure Of Human Dicer Platform-Paz-Connector Helix Casset Complex With 17-Mer Sirna Having 5'-P And Uu-3' Ends (3.1 A Resolution)
authors D.K.Simanshu, Y.Tian, D.J.Patel
compound source
Molecule: Endoribonuclease Dicer
Chain: A, B, C, D
Fragment: Platform-Paz-Connector Helix Cassette (Unp Residu 1065);
Synonym: Helicase With Rnase Motif, Helicase Moi
Ec: 3.1.26.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dicer, Dicer1, Herna, Kiaa0928
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b

Molecule: 5'-R(Pupcpgpapapgpgpupcpcpupupcpgp 3';
Chain: E, F, G, H
Engineered: Yes
Other_details: Sirna

Synthetic: Yes
symmetry Space Group: C 2 2 21
R_factor 0.223 R_Free 0.270
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.245 104.191 368.640 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.10 Å
ligand
enzyme Hydrolase E.C.3.1.26 BRENDA
Primary referenceA Phosphate-Binding Pocket within the Platform-PAZ-Connector Helix Cassette of Human Dicer., Tian Y, Simanshu DK, Ma JB, Park JE, Heo I, Kim VN, Patel DJ, Mol Cell. 2014 Feb 20;53(4):606-16. doi: 10.1016/j.molcel.2014.01.003. Epub 2014 , Jan 30. PMID:24486018
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (408 Kb) [Save to disk]
  • Biological Unit Coordinates (4ngf.pdb1.gz) 116 Kb
  • Biological Unit Coordinates (4ngf.pdb2.gz) 117 Kb
  • Biological Unit Coordinates (4ngf.pdb3.gz) 201 Kb
  • Biological Unit Coordinates (4ngf.pdb4.gz) 203 Kb
  • CSU: Contacts of Structural Units for 4NGF
  • Structure Factors (224 Kb)
  • Retrieve 4NGF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4NGF from S2C, [Save to disk]
  • Re-refined 4ngf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4NGF 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 4NGF
  • 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
  • 3D motif for 4NGF, from MSDmotif at EBI
  • Fold representative 4ngf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ngf_C] [4ngf_A] [4ngf_G] [4ngf_E] [4ngf_F] [4ngf_H] [4ngf_B] [4ngf_D] [4ngf]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4NGF: [PAZ ] by SMART
  • Other resources with information on 4NGF
  • Community annotation for 4NGF at PDBWiki (http://pdbwiki.org)

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