3PTA	Transferase Dna	date	Dec 02, 2010
title	Crystal Structure Of Human Dnmt1(646-1600) In Complex With D
authors	J.Song, D.J.Patel
compound		source
Molecule: Dna (Cytosine-5)-Methyltransferase 1 Chain: A Fragment: Unp Residues 646-1600 Synonym: Dnmt1, Cxxc-Type Zinc Finger Protein 9, Dna Methyltransferase Hsai, Dna Mtase Hsai, M.Hsai, Mcmt; Ec: 2.1.1.37 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Dnmt1, Aim, Cxxc9, Dnmt Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: C41(De3)
Molecule: Dna (5'- D(Tpcpcpcpgptpgpapgpcpcptpcpcpgpcpapgpg) Chain: B Engineered: Yes		Synthetic: Yes
Molecule: Dna (5'- D(Cpcptpgpcpgpgpapgpgpcptpcpapcpgpgpgpa) Chain: C Engineered: Yes		Synthetic: Yes
symmetry	Space Group: C 1 2 1	R_factor 0.257 R_Free 0.291
crystal cell	length a length b length c angle alpha angle beta angle gamma 162.800 87.900 113.900 90.00 97.20 90.00
method	X-Ray Diffraction	resolution	3.60 Å
ligand	SAH, ZN BindingDB	enzyme	Transferase E.C.2.1.1.37 BRENDA
Primary reference	Structure of DNMT1-DNA Complex Reveals a Role for Autoinhibition in Maintenance DNA Methylation., Song J, Rechkoblit O, Bestor TH, Patel DJ, Science. 2010 Dec 16. PMID:21163962

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (156 Kb) [Save to disk] Biological Unit Coordinates (3pta.pdb1.gz) 150 Kb LPC: Ligand-Protein Contacts for 3PTA CSU: Contacts of Structural Units for 3PTA Structure Factors (121 Kb) Retrieve 3PTA in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3PTA from S2C, [Save to disk] Re-refined 3pta structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3PTA 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 3PTA

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

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3pta_A] [3pta_B] [3pta_C] SWISS-PROT database: Domain organization of by SWISSPFAM Alignments of the sequence of 3PTA with the sequences similar proteins can be viewed for 3PTA'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 3PTA

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

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