3G03 Cell Cycle date Jan 27, 2009
title Structure Of Human Mdm2 In Complex With High Affinity Peptide
authors A.L.Czarna, G.M.Popowicz, T.A.Holak
compound source
Molecule: E3 Ubiquitin-Protein Ligase Mdm2
Chain: A, C
Fragment: N-Terminal P53 Binding Domain, Unp Residues 18- 125;
Synonym: P53-Binding Protein Mdm2, Oncoprotein Mdm2, Double Minute 2 Protein, Hdm2;
Ec: 6.3.2.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mdm2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-20b

Molecule: High Affinity Synthetic Peptide
Chain: B, D
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Peptide
symmetry Space Group: P 21 21 21
R_factor 0.210 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.360 60.170 71.020 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand
enzyme Ligase E.C.6.3.2 BRENDA
Primary referenceHot, hotter, hottest., Domling A, Cell Cycle. 2009 Apr 15;8(8):1112. Epub 2009 Apr 15. PMID:19342883
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (40 Kb) [Save to disk]
  • Biological Unit Coordinates (3g03.pdb1.gz) 19 Kb
  • Biological Unit Coordinates (3g03.pdb2.gz) 18 Kb
  • CSU: Contacts of Structural Units for 3G03
  • Likely Quarternary Molecular Structure file(s) for 3G03
  • Structure Factors (113 Kb)
  • Retrieve 3G03 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3G03 from S2C, [Save to disk]
  • Re-refined 3g03 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3G03 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 3G03
  • 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 3G03, from MSDmotif at EBI
  • Fold representative 3g03 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3g03_D] [3g03] [3g03_A] [3g03_B] [3g03_C]
  • SWISS-PROT database: [Q00987]
  • Domain organization of [MDM2_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 3G03 with the sequences similar proteins can be viewed for 3G03's classification [MDM2_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [MDM2_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3G03
  • Community annotation for 3G03 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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