1T4F Ligase date Apr 29, 2004
title Structure Of Human Mdm2 In Complex With An Optimized P53 Peptide
authors B.L.Grasberger, C.Schubert, H.K.Koblish, T.E.Carver, C.F.Franks, S.Y.Zhao, T.Lu, L.V.Lafrance, D.J.Parks
compound source
Molecule: Ubiquitin-Protein Ligase E3 Mdm2
Chain: M
Synonym: P53-Binding Protein Mdm2, Oncoprotein Mdm2, Double Minute 2 Protein, Hdm2;
Ec: 6.3.2.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mdm2
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Pgex4t-3

Molecule: Optimized P53 Peptide
Chain: P
Engineered: Yes

symmetry Space Group: P 21 21 21
R_factor 0.197 R_Free 0.231
length a length b length c angle alpha angle beta angle gamma
41.030 43.590 54.570 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand SO4 enzyme Ligase E.C.6.3.2 BRENDA
related structures by homologous chain: 1YCQ

Primary referenceDiscovery and cocrystal structure of benzodiazepinedione HDM2 antagonists that activate p53 in cells., Grasberger BL, Lu T, Schubert C, Parks DJ, Carver TE, Koblish HK, Cummings MD, LaFrance LV, Milkiewicz KL, Calvo RR, Maguire D, Lattanze J, Franks CF, Zhao S, Ramachandren K, Bylebyl GR, Zhang M, Manthey CL, Petrella EC, Pantoliano MW, Deckman IC, Spurlino JC, Maroney AC, Tomczuk BE, Molloy CJ, Bone RF, J Med Chem 2005 Feb 24;48(4):909-12. PMID:15715460
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (23 Kb) [Save to disk]
  • Biological Unit Coordinates (1t4f.pdb1.gz) 19 Kb
  • LPC: Ligand-Protein Contacts for 1T4F
  • CSU: Contacts of Structural Units for 1T4F
  • Likely Quarternary Molecular Structure file(s) for 1T4F
  • Structure Factors (83 Kb)
  • Retrieve 1T4F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1T4F from S2C, [Save to disk]
  • Re-refined 1t4f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1T4F 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 1T4F
  • 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 1T4F, from MSDmotif at EBI
  • Fold representative 1t4f from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1t4f] [1t4f_P] [1t4f_M]
  • SWISS-PROT database: [Q00987]
  • Domain organization of [MDM2_HUMAN] by SWISSPFAM
  • Other resources with information on 1T4F
  • Community annotation for 1T4F 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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