3D05	Transcription	date	May 01, 2008
title	Human P53 Core Domain With Hot Spot Mutation R249s (II)
authors	O.Suad, H.Rozenberg, L.J.W.Shimon, F.Frolow, Z.Shakked
compound		source
Molecule: Cellular Tumor Antigen P53 Chain: A Fragment: P53 Core Domain, Unp Residues 94-293 Synonym: Tumor Suppressor P53, Phosphoprotein P53, Antigen Ny-Co-13; Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Tp53 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet27-B
symmetry	Space Group: P 65 2 2	R_factor 0.218 R_Free 0.264
crystal cell	length a length b length c angle alpha angle beta angle gamma 44.374 44.374 330.026 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	1.70 Å
ligand	ZN	enzyme
Primary reference	Structural basis of restoring sequence-specific DNA binding and transactivation to mutant p53 by suppressor mutations., Suad O, Rozenberg H, Brosh R, Diskin-Posner Y, Kessler N, Shimon LJ, Frolow F, Liran A, Rotter V, Shakked Z, J Mol Biol. 2009 Jan 9;385(1):249-65. Epub 2008 Oct 30. PMID:18996393

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (38 Kb) [Save to disk] Biological Unit Coordinates (3d05.pdb1.gz) 34 Kb LPC: Ligand-Protein Contacts for 3D05 CSU: Contacts of Structural Units for 3D05 Likely Quarternary Molecular Structure file(s) for 3D05 Structure Factors (321 Kb) Retrieve 3D05 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3D05 from S2C, [Save to disk] Re-refined 3d05 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3D05 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 3D05

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 3D05, from MSDmotif at EBI Fold representative 3d05 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3d05_A] SWISS-PROT database: [P04637] Domain organization of [P53_HUMAN] by SWISSPFAM Alignments of the sequence of 3D05 with the sequences similar proteins can be viewed for 3D05's classification [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 [P53_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 3D05

Community annotation for 3D05 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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