3OL2	Signaling Protein	date	Aug 25, 2010
title	Receptor-Ligand Structure Of Human Semaphorin 4d With Plexin
authors	B.J.C.Janssen, R.A.Robinson, F.Perez-Branguli, C.H.Bell, C.J.Mit C.Siebold, E.Y.Jones
compound		source
Molecule: Semaphorin-4d Chain: A Fragment: Extracellular Domains Synonym: Bb18, A8, Gr3 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Sema4d, C9orf164, Cd100, Semaj Expression_system: Homo Sapiens Expression_system_common: Human Expression_system_taxid: 9606
Molecule: Plexin-B1 Chain: B Fragment: Extracellular Domainsl (1-2) Synonym: Semaphorin Receptor Sep Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Plxnb1, Kiaa0407, Plxn5, Sep Expression_system: Homo Sapiens Expression_system_common: Human Expression_system_taxid: 9606
symmetry	Space Group: F 2 2 2	R_factor 0.190 R_Free 0.237
crystal cell	length a length b length c angle alpha angle beta angle gamma 83.055 173.436 482.119 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.99 Å
ligand	BMA, NAG	enzyme
Gene Ontology	Chain Function Process Component A B
Primary reference	Structural basis of semaphorin-plexin signalling., Janssen BJ, Robinson RA, Perez-Branguli F, Bell CH, Mitchell KJ, Siebold C, Jones EY, Nature. 2010 Sep 26. PMID:20877282

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (377 Kb) [Save to disk] Biological Unit Coordinates (3ol2.pdb1.gz) 731 Kb LPC: Ligand-Protein Contacts for 3OL2 CSU: Contacts of Structural Units for 3OL2 Structure Factors (295 Kb) Retrieve 3OL2 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3OL2 from S2C, [Save to disk] Re-refined 3ol2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3OL2 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 3OL2

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 3OL2, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3ol2_A] [3ol2_B] [3ol2] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 3OL2: [IG] [PSI] [Sema ] by SMART

Other resources with information on 3OL2

Community annotation for 3OL2 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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