1SOA	Protein Binding	date	Mar 13, 2004
title	Human Dj-1 With Sulfinic Acid
authors	R.Canet-Aviles, M.A.Wilson, D.W.Miller, R.Ahmad, C.Mclendon, S.Bandyopadhyay, M.J.Baptista, D.Ringe, G.A.Petsko, M.R.Cookson
compound		source
Molecule: Rna-Binding Protein Regulatory Subunit; Oncogene Chain: A Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet15b
symmetry	Space Group: P 31 2 1	R_factor R_Free
crystal cell	length a length b length c angle alpha angle beta angle gamma 75.130 75.130 75.094 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	1.20 Å
ligand	CSW	enzyme
related structures	by homologous chain: 1P5F, 1Q2U
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	The Parkinson's disease protein DJ-1 is neuroprotective due to cysteine-sulfinic acid-driven mitochondrial localization., Canet-Aviles RM, Wilson MA, Miller DW, Ahmad R, McLendon C, Bandyopadhyay S, Baptista MJ, Ringe D, Petsko GA, Cookson MR, Proc Natl Acad Sci U S A 2004 Jun 15;101(24):9103-8. Epub 2004 Jun 4. PMID:15181200

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (76 Kb) [Save to disk] Biological Unit Coordinates (1soa.pdb1.gz) 144 Kb LPC: Ligand-Protein Contacts for 1SOA CSU: Contacts of Structural Units for 1SOA Likely Quarternary Molecular Structure file(s) for 1SOA Structure Factors (1073 Kb) Retrieve 1SOA in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1SOA from S2C, [Save to disk] Re-refined 1soa structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1SOA 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 1SOA

Cartoon representation from PDB Cartoon Ramachandran plot from PDBSum

Structure-derived information

Conformational Epitope Prediction for 1SOA from the CEP Server. 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 1SOA, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1soaa_, region A [Jmol] [rasmolscript] [script source] Fold representative 1soa from FSSP and Dali (Families of Structurally Similar Proteins) Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1soa_A] SWISS-PROT database: [Q99497] Domain organization of [PARK7_HUMAN] by SWISSPFAM Alignments of the sequence of 1SOA with the sequences similar proteins can be viewed for 1SOA'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 1SOA

Community annotation for 1SOA at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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