5MNJ Ligase date Dec 13, 2016
title Structure Of Mdm2-Mdmx-Ubch5b-Ubiquitin Complex
authors M.Klejnot, D.T.Huang
compound source
Molecule: Ubiquitin-Conjugating Enzyme E2 D2
Chain: A, E
Synonym: (E3-Independent) E2 Ubiquitin-Conjugating Enzyme D Ubiquitin-Conjugating Enzyme D2,Ubiquitin Carrier Protein D Ubiquitin-Conjugating Enzyme E2(17)Kb 2,Ubiquitin-Conjugati E2-17 Kda 2,Ubiquitin-Protein Ligase D2,P53-Regulated Ubiqu Conjugating Enzyme 1;
Ec: 2.3.2.23,2.3.2.24
Engineered: Yes
Mutation: Yes
Other_details: K85 In Chains A And E Form Isopeptide Linkag Carbonyl Carbon Of G76 In Chains B And F, Respectively.;
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ube2d2, Pubc1, Ubc4, Ubc5b, Ubch4, Ubch5b
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Polyubiquitin-B
Chain: B, F
Engineered: Yes
Other_details: Gsggs Linker At The N-Terminus Resulted From G76 In Chain B Is Covalently Linked To K85 Side Chain In Ch
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ubb
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: E3 Ubiquitin-Protein Ligase Mdm2
Chain: C, G
Synonym: Double Minute 2 Protein,Hdm2,Oncoprotein Mdm2,P53- Protein Mdm2;
Ec: 6.3.2.-
Engineered: Yes
Other_details: Contains N-Terminal His-Tag Followed By Tev Cleavage Site That Was Not Removed During Purification. Mdm 428-491.;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mdm2
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Protein Mdm4
Chain: D, H
Synonym: Double Minute 4 Protein,Mdm2-Like P53-Binding Prot Protein Mdmx,P53-Binding Protein Mdm4;
Engineered: Yes
Other_details: Mdmx Contains 427-490
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mdm4, Mdmx
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor 0.190 R_Free 0.231
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.240 62.760 66.350 69.83 69.22 78.21
method X-Ray Diffractionresolution 2.16 Å
ligand SO4, ZN enzyme Transferase E.C.2.3.2.23 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


H, D


Primary referenceStructural analysis of MDM2 RING separates degradation from regulation of p53 transcription activity., Nomura K, Klejnot M, Kowalczyk D, Hock AK, Sibbet GJ, Vousden KH, Huang DT, Nat Struct Mol Biol. 2017 Jul;24(7):578-587. doi: 10.1038/nsmb.3414. Epub 2017, May 29. PMID:28553961
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (115 Kb) [Save to disk]
  • Biological Unit Coordinates (5mnj.pdb1.gz) 54 Kb
  • Biological Unit Coordinates (5mnj.pdb2.gz) 56 Kb
  • LPC: Ligand-Protein Contacts for 5MNJ
  • CSU: Contacts of Structural Units for 5MNJ
  • Structure Factors (1570 Kb)
  • Retrieve 5MNJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5MNJ from S2C, [Save to disk]
  • Re-refined 5mnj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5MNJ 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 5MNJ
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5mnj_E] [5mnj_G] [5mnj_A] [5mnj_B] [5mnj_H] [5mnj_C] [5mnj_D] [5mnj_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5MNJ
  • Community annotation for 5MNJ at PDBWiki (http://pdbwiki.org)

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