3HM6	Signaling Protein	date	May 28, 2009
title	Crystal Structure Of The Cytoplasmic Domain Of Human Plexin
authors	Y.Tong, H.He, L.Shen, W.Tempel, F.Mackenzie, C.H.Arrowsmith, A.M.E C.Bountra, J.Weigelt, A.Bochkarev, H.Park, Structural Genomics Consortium (Sgc)
compound		source
Molecule: Plexin-B1 Chain: X Fragment: Cytoplasmic Domain (Unp Residues 1511-2135) Synonym: Semaphorin Receptor Sep Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Plxnb1, Kiaa0407, Plxn5, Sep Expression_system: Spodoptera Frugiperda Expression_system_common: Fall Armyworm Expression_system_taxid: 7108 Expression_system_strain: Sf9 Expression_system_plasmid: Pfboh-Lic (Gi:134105591)
Molecule: Unknown Peptide Chain: C Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Plxnb1, Kiaa0407, Plxn5, Sep Expression_system: Spodoptera Frugiperda Expression_system_common: Fall Armyworm Expression_system_taxid: 7108 Expression_system_strain: Sf9 Expression_system_plasmid: Pfboh-Lic (Gi:134105591)
symmetry	Space Group: P 31 2 1	R_factor 0.227 R_Free 0.262
crystal cell	length a length b length c angle alpha angle beta angle gamma 74.346 74.346 214.398 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.40 Å
ligand	UNX	enzyme
Gene Ontology	Chain Function Process Component X
Primary reference	Structure and function of the intracellular region of the plexin-B1 transmembrane receptor., Tong Y, Hota PK, Penachioni JY, Hamaneh MB, Kim S, Alviani R, Shen L, He H, Tempel W, Tamagnone L, Park HW, Buck M, J Biol Chem. 2009 Oct 22. PMID:19843518

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (89 Kb) [Save to disk] Biological Unit Coordinates (3hm6.pdb1.gz) 83 Kb LPC: Ligand-Protein Contacts for 3HM6 CSU: Contacts of Structural Units for 3HM6 Likely Quarternary Molecular Structure file(s) for 3HM6 Structure Factors (411 Kb) Retrieve 3HM6 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3HM6 from S2C, [Save to disk] Re-refined 3hm6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3HM6 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 3HM6

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 3HM6, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3hm6] [3hm6_X] [3hm6_C] SWISS-PROT database: [O43157] Domain organization of [PLXB1_HUMAN] by SWISSPFAM

Other resources with information on 3HM6

Community annotation for 3HM6 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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