4MDK Ligase Ligase Inhibitor date Aug 22, 2013
title Cdc34-Ubiquitin-Cc0651 Complex
authors D.F.Ceccarelli, S.Orlicky, M.Tyers, F.Sicheri
compound source
Molecule: Ubiquitin-Conjugating Enzyme E2 R1
Chain: A, B, C, D
Fragment: E2 Domain (Unp Residues 7-184)
Synonym: Ubiquitin-Conjugating Enzyme E2-32 Kda Complementi Ubiquitin-Conjugating Enzyme E2-Cdc34, Ubiquitin-Protein Li
Ec: 6.3.2.19
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cdc34, Ubch3, Ube2r1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Proex

Molecule: Ubiquitin
Chain: E, F, G, H
Fragment: Unp Residues 76-152
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ubc
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petm30
symmetry Space Group: P 1
R_factor 0.204 R_Free 0.259
crystal
cell
length a length b length c angle alpha angle beta angle gamma
55.403 72.220 75.912 71.89 79.63 81.61
method X-Ray Diffractionresolution 2.61 Å
ligand U94 enzyme Ligase E.C.6.3.2.19 BRENDA
Primary referenceE2 enzyme inhibition by stabilization of a low-affinity interface with ubiquitin., Huang H, Ceccarelli DF, Orlicky S, St-Cyr DJ, Ziemba A, Garg P, Plamondon S, Auer M, Sidhu S, Marinier A, Kleiger G, Tyers M, Sicheri F, Nat Chem Biol. 2013 Dec 15. doi: 10.1038/nchembio.1412. PMID:24316736
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (336 Kb) [Save to disk]
  • Biological Unit Coordinates (4mdk.pdb1.gz) 85 Kb
  • Biological Unit Coordinates (4mdk.pdb2.gz) 82 Kb
  • Biological Unit Coordinates (4mdk.pdb3.gz) 85 Kb
  • Biological Unit Coordinates (4mdk.pdb4.gz) 80 Kb
  • LPC: Ligand-Protein Contacts for 4MDK
  • CSU: Contacts of Structural Units for 4MDK
  • Structure Factors (450 Kb)
  • Retrieve 4MDK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4MDK from S2C, [Save to disk]
  • Re-refined 4mdk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4MDK 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 4MDK
  • 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 4MDK, from MSDmotif at EBI
  • Fold representative 4mdk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4mdk_G] [4mdk_F] [4mdk_E] [4mdk_D] [4mdk] [4mdk_C] [4mdk_H] [4mdk_A] [4mdk_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4MDK: [UBCc] [UBQ ] by SMART
  • Other resources with information on 4MDK
  • Community annotation for 4MDK at PDBWiki (http://pdbwiki.org)

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