4PEI Hydrolase Rna date Apr 23, 2014
title Dbr1 In Complex With Synthetic Branched Rna Analog
authors E.J.Montemayor, A.Katolik, N.E.Clark, A.B.Taylor, J.P.Schuermann D.J.Combs, R.Johnsson, S.P.Holloway, S.W.Stevens, M.J.Damha, P.J
compound source
Molecule: Rna Lariat Debranching Enzyme, Putative
Chain: A, B, C, D, E
Engineered: Yes
Mutation: Yes
Organism_scientific: Entamoeba Histolytica
Organism_taxid: 5759
Gene: Ehi_062730
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Yep351

Molecule: Rna (5'-R(Upapapcpa)-3')
Chain: V, W, X, Y, Z
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Rna (5'-R((G46)Pu)-3')
Chain: Q, R, S, T, U
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.184 R_Free 0.229
crystal
cell
length a length b length c angle alpha angle beta angle gamma
73.037 142.479 214.665 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand G46, GOL, NI, PG4, SO4 enzyme
Gene EHI
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, E, B
  • RNA lariat debranching enzym...


  • Primary referenceStructural basis of lariat RNA recognition by the intron debranching enzyme Dbr1., Montemayor EJ, Katolik A, Clark NE, Taylor AB, Schuermann JP, Combs DJ, Johnsson R, Holloway SP, Stevens SW, Damha MJ, Hart PJ, Nucleic Acids Res. 2014 Aug 14. pii: gku725. PMID:25123664
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (335 Kb) [Save to disk]
  • Biological Unit Coordinates (4pei.pdb1.gz) 71 Kb
  • Biological Unit Coordinates (4pei.pdb2.gz) 70 Kb
  • Biological Unit Coordinates (4pei.pdb3.gz) 71 Kb
  • Biological Unit Coordinates (4pei.pdb4.gz) 70 Kb
  • Biological Unit Coordinates (4pei.pdb5.gz) 70 Kb
  • LPC: Ligand-Protein Contacts for 4PEI
  • CSU: Contacts of Structural Units for 4PEI
  • Structure Factors (3058 Kb)
  • Retrieve 4PEI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4PEI from S2C, [Save to disk]
  • Re-refined 4pei structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4PEI 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 4PEI
  • 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 4PEI, from MSDmotif at EBI
  • Fold representative 4pei from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4pei_C] [4pei_Z] [4pei_D] [4pei] [4pei_Q] [4pei_A] [4pei_T] [4pei_S] [4pei_Y] [4pei_X] [4pei_E] [4pei_R] [4pei_W] [4pei_V] [4pei_U] [4pei_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4PEI
  • Community annotation for 4PEI at PDBWiki (http://pdbwiki.org)

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