5K77 Hydrolase Rna date May 25, 2016
title Dbr1 In Complex With 7-Mer Branched Rna
authors N.E.Clark, A.B.Taylor, P.J.Hart
compound source
Molecule: Rna Lariat Debranching Enzyme, Putative
Chain: A, B, C, D, E
Engineered: Yes
Organism_scientific: Entamoeba Histolytica
Organism_taxid: 5759
Gene: Ehi_062730
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Branch 1 Of Branched Rna 5'-Uaa(-2'Gu)Ca-3'
Chain: V, W, X, Y, Z
Engineered: Yes
Other_details: This Is A 2' Branched Rna 5'-Uaa(-2'Gu)Ca-3'

Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: Brnch 2 Of Branched Rna 5'-Uaa(-2'Gu)Ca-3'
Chain: v, w, x, y, z
Engineered: Yes
Other_details: This Is A 2' Branched Rna 5'-Uaa(-2'Gu)Ca-3'

Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932
symmetry Space Group: P 21 21 21
R_factor 0.182 R_Free 0.223
crystal
cell
length a length b length c angle alpha angle beta angle gamma
73.151 141.892 212.511 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.17 Å
ligand FE2, OH, SO4, ZN enzyme
Gene EHI
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, E, B
  • RNA lariat debranching enzym...


  • Primary referenceMetal dependence and branched RNA cocrystal structures of the RNA lariat debranching enzyme Dbr1., Clark NE, Katolik A, Roberts KM, Taylor AB, Holloway SP, Schuermann JP, Montemayor EJ, Stevens SW, Fitzpatrick PF, Damha MJ, Hart PJ, Proc Natl Acad Sci U S A. 2016 Dec 20;113(51):14727-14732. doi:, 10.1073/pnas.1612729114. Epub 2016 Dec 6. PMID:27930312
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (644 Kb) [Save to disk]
  • Biological Unit Coordinates (5k77.pdb1.gz) 131 Kb
  • Biological Unit Coordinates (5k77.pdb2.gz) 133 Kb
  • Biological Unit Coordinates (5k77.pdb3.gz) 133 Kb
  • Biological Unit Coordinates (5k77.pdb4.gz) 132 Kb
  • Biological Unit Coordinates (5k77.pdb5.gz) 134 Kb
  • LPC: Ligand-Protein Contacts for 5K77
  • CSU: Contacts of Structural Units for 5K77
  • Structure Factors (2179 Kb)
  • Retrieve 5K77 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5K77 from S2C, [Save to disk]
  • Re-refined 5k77 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5K77 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 5K77
  • 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 5k77 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5k77] [5k77_X] [5k77_v] [5k77_B] [5k77_Z] [5k77_Y] [5k77_w] [5k77_y] [5k77_W] [5k77_x] [5k77_E] [5k77_z] [5k77_A] [5k77_D] [5k77_V] [5k77_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5K77
  • Community annotation for 5K77 at PDBWiki (http://pdbwiki.org)

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