1Q47	Signaling Protein	date	Aug 01, 2003
title	Structure Of The Semaphorin 3a Receptor-Binding Module
authors	A.Antipenko, J.P.Himanen, K.Van Leyen, V.Nardi-Dei, J.Lesniak, W.A.Barton, K.R.Rajashankar, M.Lu, C.Hoemme, A.Puschel, D.Nikolo
compound		source
Molecule: Semaphorin 3a Chain: A, B Fragment: Sema-3a 65k (Residues 26-520) Synonym: Semaphorin III, Sema III, Semaphorin D, Sema D Engineered: Yes		Organism_scientific: Mus Musculus Organism_common: House Mouse Organism_taxid: 10090 Expression_system: Spodoptera Frugiperda Expression_system_common: Fall Armyworm Expression_system_taxid: 7108 Expression_system_cell_line: Sf9 Expression_system_vector_type: Baculovirus
symmetry	Space Group: C 1 2 1	R_factor 0.249 R_Free 0.294
crystal cell	length a length b length c angle alpha angle beta angle gamma 218.791 59.733 122.715 90.00 109.01 90.00
method	X-Ray Diffraction	resolution	2.80 Å
ligand	NAG	enzyme
Gene Ontology	Chain Function Process Component A, B
Primary reference	Structure of the semaphorin-3A receptor binding module., Antipenko A, Himanen JP, van Leyen K, Nardi-Dei V, Lesniak J, Barton WA, Rajashankar KR, Lu M, Hoemme C, Puschel AW, Nikolov DB, Neuron 2003 Aug 14;39(4):589-98. PMID:12925274

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (163 Kb) [Save to disk] Biological Unit Coordinates (1q47.pdb1.gz) 157 Kb LPC: Ligand-Protein Contacts for 1Q47 CSU: Contacts of Structural Units for 1Q47 Likely Quarternary Molecular Structure file(s) for 1Q47 Retrieve 1Q47 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1Q47 from S2C, [Save to disk]

View 1Q47 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 1Q47

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1Q47, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1q47a_, region A [Jmol] [rasmolscript] [script source]     - Domain d1q47b_, region B [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1q47] [1q47_B] [1q47_A] SWISS-PROT database: [O08665] Domain organization of [SEM3A_MOUSE] by SWISSPFAM Domain found in 1Q47: [Sema ] by SMART

Other resources with information on 1Q47

Community annotation for 1Q47 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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