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 0.239
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.
  • 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 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
  • Alignments of the sequence of 3KMD with the sequences similar proteins can be viewed for 3KMD's classification 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 at ProtoMap. Click on the Cluster number.
  • 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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