3CMM Ligase Protein Binding date Mar 23, 2008
title Crystal Structure Of The Uba1-Ubiquitin Complex
authors I.Lee, H.Schindelin
compound source
Molecule: Ubiquitin-Activating Enzyme E1 1
Chain: A, C
Fragment: Residues 10-1024
Ec: 6.3.2.19
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Gene: Uba1
Expression_system: Escherichia Coli
Expression_system_strain: Bl21 Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: Ubiquitin
Chain: B, D
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Gene: Ubi1, Rpl40a
Expression_system: Escherichia Coli
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ptxb1
symmetry Space Group: P 21 21 21
R_factor 0.191 R_Free 0.247
crystal
cell
length a length b length c angle alpha angle beta angle gamma
115.363 118.564 207.567 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand PRO enzyme Ligase E.C.6.3.2.19 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


Primary referenceStructural insights into E1-catalyzed ubiquitin activation and transfer to conjugating enzymes., Lee I, Schindelin H, Cell. 2008 Jul 25;134(2):268-78. PMID:18662542
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (342 Kb) [Save to disk]
  • Biological Unit Coordinates (3cmm.pdb1.gz) 170 Kb
  • Biological Unit Coordinates (3cmm.pdb2.gz) 169 Kb
  • LPC: Ligand-Protein Contacts for 3CMM
  • CSU: Contacts of Structural Units for 3CMM
  • Likely Quarternary Molecular Structure file(s) for 3CMM
  • Structure Factors (617 Kb)
  • Retrieve 3CMM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3CMM from S2C, [Save to disk]
  • Re-refined 3cmm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3CMM 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 3CMM
  • 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 3CMM, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3cmm_D] [3cmm_A] [3cmm_B] [3cmm] [3cmm_C]
  • SWISS-PROT database: [P22515] [P61864]
  • Domain organization of [UBA1_YEAST] [UBIQ_YEAST] by SWISSPFAM
  • Domains found in 3CMM: [UBA_e1_C] [UBQ ] by SMART
  • Other resources with information on 3CMM
  • Community annotation for 3CMM 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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