1OBY	Cell Adhesion	date	Jan 31, 2003
title	Crystal Structure Of The Complex Of Pdz2 Of Syntenin With A Peptide.
authors	B.S.Kang, D.R.Cooper, Y.Devedjiev, U.Derewenda, Z.S.Derewenda
compound		source
Molecule: Syntenin 1 Chain: A, B Fragment: Pdz2, Residues 197-270 Synonym: Syndecan Binding Protein 1, Melanoma Differentiati Associated Protein-9, Mda-9, Scaffold Protein Pbp1, Tacip18 Alpha Cytoplasmic Domain-Interacting Protein 18; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Atcc: 72537 Expression_system: Escherichia Coli Expression_system_taxid: 511693 Expression_system_strain: Bl21 Expression_system_vector: Pgst-Parallel1
Molecule: Syndecan-4 Chain: P, Q Fragment: Last 6 Residues, Residues 193-198 Synonym: Amphiglycan, Synd4, Ryudocan Core Protein Engineered: Yes		Synthetic: Yes Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606
symmetry	Space Group: C 1 2 1	R_factor 0.175 R_Free 0.226
crystal cell	length a length b length c angle alpha angle beta angle gamma 58.337 54.441 50.219 90.00 98.65 90.00
method	X-Ray Diffraction	resolution	1.85 Å
ligand	SO4	enzyme
related structures	by homologous chain: 1N99, 1V1T
Gene Ontology	Chain Function Process Component A, B
Primary reference	Molecular roots of degenerate specificity in syntenin's PDZ2 domain: reassessment of the PDZ recognition paradigm., Kang BS, Cooper DR, Devedjiev Y, Derewenda U, Derewenda ZS, Structure (Camb) 2003 Jul;11(7):845-53. PMID:12842047

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (34 Kb) [Save to disk] Biological Unit Coordinates (1oby.pdb1.gz) 28 Kb LPC: Ligand-Protein Contacts for 1OBY CSU: Contacts of Structural Units for 1OBY Likely Quarternary Molecular Structure file(s) for 1OBY Structure Factors (180 Kb) Retrieve 1OBY in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1OBY from S2C, [Save to disk] Re-refined 1oby structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1OBY 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 1OBY

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1OBY, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1obya_, region A [Jmol] [rasmolscript] [script source]     - Domain d1obyb_, region B [Jmol] [rasmolscript] [script source] 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: [1oby] [1oby_B] [1oby_P] [1oby_Q] [1oby_A] SWISS-PROT database: [P31431] [O00560] Belongs to the ezrin/radixin/moesin-binding phosphoprotein 50 (ebp50) family according to TCDB. Belongs to the peptide translocating syndecan (syndecan) family according to TCDB. Domain organization of [SDC4_HUMAN] [SDCB1_HUMAN] by SWISSPFAM Domain found in 1OBY: [PDZ ] by SMART

Other resources with information on 1OBY

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

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