2H0D Metal Binding Protein Ligase date May 14, 2006
title Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin Ligase
authors R.M.Xu
compound source
Molecule: B Lymphoma Mo-Mlv Insertion Region
Chain: A
Fragment: Residues 5-101
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-Kg-6p

Molecule: Ubiquitin Ligase Protein Ring2
Chain: B
Fragment: Residues 15-114
Synonym: Ring Finger Protein 2, Ring Finger Protein 1b, Rin Finger Protein Bap-1, Ding Protein, Huntingtin-Interacting Interacting Protein 3, Hip2-Interacting Protein 3;
Ec: 6.3.2.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcdfduet-1
symmetry Space Group: P 63
R_factor 0.210 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
120.514 120.514 27.209 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.50 Å
ligand ZN enzyme Ligase E.C.6.3.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
B


Primary referenceStructure of a Bmi-1-Ring1B polycomb group ubiquitin ligase complex., Li Z, Cao R, Wang M, Myers MP, Zhang Y, Xu RM, J Biol Chem. 2006 Jul 21;281(29):20643-9. Epub 2006 May 18. PMID:16714294
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (39 Kb) [Save to disk]
  • Biological Unit Coordinates (2h0d.pdb1.gz) 33 Kb
  • LPC: Ligand-Protein Contacts for 2H0D
  • CSU: Contacts of Structural Units for 2H0D
  • Likely Quarternary Molecular Structure file(s) for 2H0D
  • Structure Factors (197 Kb)
  • Retrieve 2H0D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2H0D from S2C, [Save to disk]
  • Re-refined 2h0d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2H0D 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 2H0D
  • 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
  • 3D motif for 2H0D, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2h0d_A] [2h0d_B] [2h0d]
  • SWISS-PROT database: [P35226] [Q5T8Z3] [Q99496]
  • Domain organization of [BMI1_HUMAN] [Q5T8Z3_HUMAN] [RING2_HUMAN] by SWISSPFAM
  • Domain found in 2H0D: [RING ] by SMART
  • Other resources with information on 2H0D
  • Community annotation for 2H0D at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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