1RV1 Ligase date Dec 12, 2003
title Crystal Structure Of Human Mdm2 With An Imidazoline Inhibitor
authors C.Lukacs, U.Kammlott, B.Graves
compound source
Molecule: Ubiquitin-Protein Ligase E3 Mdm2
Chain: A, B, C
Fragment: Residues 25-109
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: Plasmid
Expression_system_plasmid: Pqe40
symmetry Space Group: C 1 2 1
R_factor 0.256 R_Free 0.322
crystal
cell
length a length b length c angle alpha angle beta angle gamma
122.264 39.727 79.362 90.00 114.29 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand IMZ BindingDB enzyme Ligase E.C.6.3.2 BRENDA
related structures by homologous chain: 1YCQ, 1YCR
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceIn vivo activation of the p53 pathway by small-molecule antagonists of MDM2., Vassilev LT, Vu BT, Graves B, Carvajal D, Podlaski F, Filipovic Z, Kong N, Kammlott U, Lukacs C, Klein C, Fotouhi N, Liu EA, Science 2004 Feb 6;303(5659):844-8. Epub 2004 Jan 2. PMID:14704432
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (52 Kb) [Save to disk]
  • Biological Unit Coordinates (1rv1.pdb1.gz) 47 Kb
  • LPC: Ligand-Protein Contacts for 1RV1
  • CSU: Contacts of Structural Units for 1RV1
  • Likely Quarternary Molecular Structure file(s) for 1RV1
  • Retrieve 1RV1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RV1 from S2C, [Save to disk]
  • View 1RV1 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 1RV1
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1RV1, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1rv1a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1rv1b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1rv1c_, region C [Jmol] [rasmolscript] [script source]
  • Fold representative 1rv1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1rv1_B] [1rv1_C] [1rv1] [1rv1_A]
  • SWISS-PROT database: [Q00987]
  • Domain organization of [MDM2_HUMAN] by SWISSPFAM
  • Other resources with information on 1RV1
  • Community annotation for 1RV1 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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