3CY6	Unknown Function	date	Apr 25, 2008
title	Crystal Structure Of E18q Dj-1
authors	A.C.Witt, M.Lakshminarasimhan, B.C.Remington, S.Hasim, E.Pozharski, M.A.Wilson
compound		source
Molecule: Protein Dj-1 Chain: A Synonym: Oncogene Dj1 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Park7 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet21a
symmetry	Space Group: P 31 2 1	R_factor 0.154 R_Free 0.168
crystal cell	length a length b length c angle alpha angle beta angle gamma 74.780 74.780 75.443 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	1.35 Å
Gene Ontology	Chain Function Process Component A RNA binding mRNA binding peroxidase activity protein binding peptidase activity hydrolase activity protein homodimerization act... peroxiredoxin activity synaptic transmission, dopam... proteolysis autophagy response to stress inflammatory response mitochondrion organization single fertilization cell death adult locomotory behavior negative regulation of prote... cellular response to oxidati... response to hydrogen peroxid... hydrogen peroxide metabolic ... regulation of neuron apoptot... negative regulation of neuro... regulation of inflammatory r... protein stabilization dopamine uptake involved in ... membrane depolarization membrane hyperpolarization negative regulation of cell ... regulation of androgen recep... cellular response to hydroge... positive regulation of oxida... negative regulation of extri... nucleus cytoplasm mitochondrion
Primary reference	Cysteine pKa depression by a protonated glutamic acid in human DJ-1., Witt AC, Lakshminarasimhan M, Remington BC, Hasim S, Pozharski E, Wilson MA, Biochemistry. 2008 Jul 15;47(28):7430-40. Epub 2008 Jun 21. PMID:18570440

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (38 Kb) [Save to disk] Biological Unit Coordinates (3cy6.pdb1.gz) 65 Kb CSU: Contacts of Structural Units for 3CY6 Likely Quarternary Molecular Structure file(s) for 3CY6 Structure Factors (376 Kb) Retrieve 3CY6 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3CY6 from S2C, [Save to disk] Re-refined 3cy6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3CY6 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 3CY6

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 3CY6, from MSDmotif at EBI Fold representative 3cy6 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3cy6_A] SWISS-PROT database: [Q99497] Domain organization of [PARK7_HUMAN] by SWISSPFAM Alignments of the sequence of 3CY6 with the sequences similar proteins can be viewed for 3CY6's classification [PARK7_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 [PARK7_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 3CY6

Community annotation for 3CY6 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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