1YCQ Complex (Oncogene Protein Peptide) date Sep 30, 1996
title Xenopus Laevis Mdm2 Bound To The Transactivation Domain Of Human P53
authors P.H.Kussie, N.P.Pavletich
compound source
Molecule: Mdm2
Chain: A
Synonym: Mdm2
Engineered: Yes
Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_plasmid: Pet3d

Molecule: P53
Chain: B
Fragment: Residues 13 - 29
Engineered: Yes

symmetry Space Group: P 63 2 2
R_factor 0.188 R_Free 0.253
crystal
cell
length a length b length c angle alpha angle beta angle gamma
84.960 84.960 63.890 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
note 1YCQ (Molecule of the Month:pdb31)
related structures by homologous chain: 1RV1, 1T4F
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain., Kussie PH, Gorina S, Marechal V, Elenbaas B, Moreau J, Levine AJ, Pavletich NP, Science 1996 Nov 8;274(5289):948-53. PMID:8875929
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (21 Kb) [Save to disk]
  • Biological Unit Coordinates (1ycq.pdb1.gz) 34 Kb
  • CSU: Contacts of Structural Units for 1YCQ
  • Likely Quarternary Molecular Structure file(s) for 1YCQ
  • Retrieve 1YCQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YCQ from S2C, [Save to disk]
  • View 1YCQ 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 1YCQ
  • 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 1YCQ, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ycqa_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1ycq 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: [1ycq_A] [1ycq] [1ycq_B]
  • SWISS-PROT database: [P56273] [P04637]
  • Belongs to the pore-forming pnc-27 peptide of 32 aas from the p53 tumor suppressor protein (pnc-27) family according to TCDB.
  • Domain organization of [MDM2_XENLA] [P53_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 1YCQ with the sequences similar proteins can be viewed for 1YCQ's classification [MDM2_XENLA] [P53_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_XENLA] [P53_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1YCQ
  • Community annotation for 1YCQ 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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