1YBO	Structural Protein	date	Dec 21, 2004
title	Crystal Structure Of The Pdz Tandem Of Human Syntenin With S Peptide
authors	J.Grembecka, D.R.Cooper, T.Cierpicki, B.S.Kang, Y.Devedjiev, Z.De
compound		source
Molecule: Syntenin 1 Chain: A, B Synonym: Syndecan Binding Protein 1, Melanoma Differentiati Associated Protein-9, Mda-9, Scaffold Protein Pbp1, Pro-Tgf Cytoplasmic Domain-Interacting Protein 18, Tacip18; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Sdcbp, Mda9, Sycl Expression_system: Escherichia Coli Bl21 Expression_system_taxid: 511693 Expression_system_strain: Bl21 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pgst-Parallel-1
Molecule: Syndecan-4 Chain: C, D Synonym: Amphiglycan, Synd4, Ryudocan Core Protein Engineered: Yes		Synthetic: Yes Other_details: Synthesized Peptide Cooresponding To The C-T Of Syndecan
symmetry	Space Group: P 41 21 2	R_factor 0.193 R_Free 0.273
crystal cell	length a length b length c angle alpha angle beta angle gamma 72.322 72.322 125.921 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.30 Å
Gene Ontology	Chain Function Process Component A, B
Primary reference	The binding of the PDZ tandem of syntenin to target proteins., Grembecka J, Cierpicki T, Devedjiev Y, Derewenda U, Kang BS, Bushweller JH, Derewenda ZS, Biochemistry. 2006 Mar 21;45(11):3674-83. PMID:16533050

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (61 Kb) [Save to disk] Biological Unit Coordinates (1ybo.pdb1.gz) 54 Kb CSU: Contacts of Structural Units for 1YBO Likely Quarternary Molecular Structure file(s) for 1YBO Structure Factors (230 Kb) Retrieve 1YBO in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1YBO from S2C, [Save to disk] Re-refined 1ybo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1YBO 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 1YBO

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 1YBO, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1ybo_C] [1ybo_A] [1ybo_D] [1ybo] [1ybo_B] 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 1YBO: [PDZ ] by SMART

Other resources with information on 1YBO

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

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