3FDE	Ligase	date	Nov 25, 2008
title	Mouse Uhrf1 Sra Domain Bound With Hemi-Methylated Cpg Dna, C Structure In Space Group C222(1) At 1.4 A Resolution
authors	H.Hashimoto, J.R.Horton, X.Zhang, X.Cheng
compound		source
Molecule: E3 Ubiquitin-Protein Ligase Uhrf1 Chain: A, B Fragment: Ydg Domain: Unp Residues 419-628 Synonym: Ubiquitin-Like Phd And Ring Finger Domain-Containi 1, Ubiquitin-Like-Containing Phd And Ring Finger Domains Pr Nuclear Zinc Finger Protein Np95, Nuclear Protein 95; Ec: 6.3.2.- Engineered: Yes		Organism_scientific: Mus Musculus Organism_taxid: 10090 Gene: Np95, Uhrf1 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pxc666
Molecule: 5'-D(Cpcpaptpgp(5cm)Pgpcptpgpapc)-3' Chain: D, C Engineered: Yes		Synthetic: Yes Other_details: Synthetic Dna Oligo
Molecule: 5'-D(Gptpcpapgpcpgpcpaptpgpg)-3' Chain: E, F Engineered: Yes		Synthetic: Yes Other_details: Synthetic Dna Oligo
symmetry	Space Group: C 2 2 21	R_factor 0.149 R_Free 0.186
crystal cell	length a length b length c angle alpha angle beta angle gamma 84.678 103.691 149.838 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.41 Å
ligand	5CM, EDO, NA, UNL	enzyme	Ligase E.C.6.3.2 BRENDA
note	3FDE is a representative structure
Primary reference	UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications., Hashimoto H, Horton JR, Zhang X, Cheng X, Epigenetics. 2009 Jan 10;4(1). PMID:19077538

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (212 Kb) [Save to disk] Biological Unit Coordinates (3fde.pdb1.gz) 103 Kb Biological Unit Coordinates (3fde.pdb2.gz) 105 Kb LPC: Ligand-Protein Contacts for 3FDE CSU: Contacts of Structural Units for 3FDE Likely Quarternary Molecular Structure file(s) for 3FDE Structure Factors (1858 Kb) Retrieve 3FDE in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3FDE from S2C, [Save to disk] Re-refined 3fde structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3FDE 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 3FDE

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 3D motif for 3FDE, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3fde_A] [3fde_E] [3fde_B] [3fde] [3fde_D] [3fde_F] [3fde_C] SWISS-PROT database: [Q8VDF2] Domain organization of [UHRF1_MOUSE] by SWISSPFAM Domain found in 3FDE: [SRA ] by SMART

Other resources with information on 3FDE

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

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