3KMD Dna Binding Protein Dna date Nov 10, 2009
title Crystal Structure Of The P53 Core Domain Bound To A Full Con Site As A Self-Assembled Tetramer
authors Y.Chen, R.Dey, L.Chen
compound source
Molecule: Cellular Tumor Antigen P53
Chain: A, B, D, C
Fragment: Unp Residues 92-291, Dna Binding Domain
Synonym: Tumor Suppressor P53, Phosphoprotein P53, Antigen
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 5'-D(Gpgpgpcpaptpgpcpcptpapgpgpcpa C)-3';
Chain: E, F
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.216 R_Free 0.240
length a length b length c angle alpha angle beta angle gamma
65.084 93.713 145.570 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand ZN enzyme
A, D, C, B

Primary referenceCrystal structure of the p53 core domain bound to a full consensus site as a self-assembled tetramer., Chen Y, Dey R, Chen L, Structure. 2010 Feb 10;18(2):246-56. PMID:20159469
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (302 Kb) [Save to disk]
  • Biological Unit Coordinates (3kmd.pdb1.gz) 298 Kb
  • LPC: Ligand-Protein Contacts for 3KMD
  • CSU: Contacts of Structural Units for 3KMD
  • Structure Factors (431 Kb)
  • Retrieve 3KMD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KMD from S2C, [Save to disk]
  • Re-refined 3kmd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3KMD in 3D
  • Proteopedia, because life has more than 2D.
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  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3KMD
  • 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 3KMD, from MSDmotif at EBI
  • Fold representative 3kmd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3kmd_C] [3kmd_E] [3kmd_B] [3kmd_A] [3kmd] [3kmd_D] [3kmd_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3KMD
  • Community annotation for 3KMD 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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