3ZRC Transcription date Jun 15, 2011
title Pvhl54-213-Elob-Eloc Complex (4r)-4-Hydroxy-1-[(3-Methylisox Yl)Acetyl]-N-[4-(1,3-Oxazol-5-Yl)Benzyl]-L-Prolinamide Boun
authors I.Van Molle, D.L.Buckley, C.M.Crews, A.Ciulli
compound source
Molecule: Transcription Elongation Factor B Polypeptide 2
Chain: A, D, G, J
Synonym: Elongin 18 Kda Subunit, Elongin-B, Elob, Rna Polym Transcription Factor Siii Subunit B, Siii P18, Elonginb;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_vector: Pcdf-Duet1

Molecule: Transcription Elongation Factor B Polypeptide 1
Chain: B, E, H, K
Fragment: 17-112
Synonym: Elongin 15 Kda Subunit, Elongin-C, Eloc, Rna Polym Transcription Factor Siii Subunit C, Siii P15, Elonginc;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_vector: Pcdf-Duet1

Molecule: Von Hippel-Lindau Disease Tumor Suppressor
Chain: C, F, I, L
Fragment: Residues 54-213
Synonym: Protein G7, Pvhl
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet28a
symmetry Space Group: P 41 2 2
R_factor 0.24224 R_Free 0.35042
crystal
cell
length a length b length c angle alpha angle beta angle gamma
93.741 93.741 363.184 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand L8B enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, J, D, G


H, K, E, B


Primary referenceTargeting the von Hippel-Lindau E3 Ubiquitin Ligase Using Small Molecules To Disrupt the VHL/HIF-1alpha Interaction., Buckley DL, Van Molle I, Gareiss PC, Tae HS, Michel J, Noblin DJ, Jorgensen WL, Ciulli A, Crews CM, J Am Chem Soc. 2012 Mar 14;134(10):4465-8. Epub 2012 Feb 27. PMID:22369643
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (218 Kb) [Save to disk]
  • Biological Unit Coordinates (3zrc.pdb1.gz) 53 Kb
  • Biological Unit Coordinates (3zrc.pdb2.gz) 54 Kb
  • Biological Unit Coordinates (3zrc.pdb3.gz) 56 Kb
  • Biological Unit Coordinates (3zrc.pdb4.gz) 56 Kb
  • LPC: Ligand-Protein Contacts for 3ZRC
  • CSU: Contacts of Structural Units for 3ZRC
  • Structure Factors (488 Kb)
  • Retrieve 3ZRC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ZRC from S2C, [Save to disk]
  • Re-refined 3zrc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3ZRC 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 3ZRC
  • 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 3ZRC, from MSDmotif at EBI
  • Fold representative 3zrc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3zrc] [3zrc_J] [3zrc_E] [3zrc_C] [3zrc_D] [3zrc_G] [3zrc_B] [3zrc_L] [3zrc_A] [3zrc_H] [3zrc_F] [3zrc_K] [3zrc_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3ZRC: [Skp1] [UBQ ] by SMART
  • Other resources with information on 3ZRC
  • Community annotation for 3ZRC at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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