2VSM	Hydrolase	date	Apr 25, 2008
title	Nipah Virus Attachment Glycoprotein In Complex With Human Ce Receptor Ephrinb2
authors	T.A.Bowden, A.R.Aricescu, R.J.Gilbert, J.M.Grimes, E.Y.Jones, D.I
compound		source
Molecule: Hemagglutinin-Neuraminidase Chain: A Fragment: B-Propeller, Ephrin Binding Domain, Residues 188- Synonym: Niv-G Ec: 3.2.1.18 Engineered: Yes Other_details: N-Acetylglucosamine Linkages Observed In		Organism_scientific: Nipah Virus Organism_taxid: 121791 Expression_system: Homo Sapiens Expression_system_taxid: 9606 Expression_system_cell_line: Hek293t Expression_system_plasmid: Phlsec Other_details: Synthetically Optimized Cdna (Geneart)
Molecule: Ephrin-B2 Chain: B Fragment: Receptor-Binding Domain, Residues 28-165 Synonym: Efnb2, Eph-Related Receptor Tyrosine Kinase Ligand 5, Htk Ligand, Htk-L; Engineered: Yes Other_details: N-Acetylglucosamine Linkage Observed In		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Homo Sapiens Expression_system_taxid: 9606 Expression_system_cell_line: Hek293t Expression_system_plasmid: Phlsec
symmetry	Space Group: P 21 21 21	R_factor 0.152 R_Free 0.198
crystal cell	length a length b length c angle alpha angle beta angle gamma 63.236 95.834 97.909 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.80 Å
ligand	IPA, NAG	enzyme	Hydrolase E.C.3.2.1.18 BRENDA
note	2VSM is a representative structure
Gene Ontology	Chain Function Process Component A B
Primary reference	Structural basis of Nipah and Hendra virus attachment to their cell-surface receptor ephrin-B2., Bowden TA, Aricescu AR, Gilbert RJ, Grimes JM, Jones EY, Stuart DI, Nat Struct Mol Biol. 2008 Jun;15(6):567-72. Epub 2008 May 18. PMID:18488039

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (112 Kb) [Save to disk] Biological Unit Coordinates (2vsm.pdb1.gz) 106 Kb LPC: Ligand-Protein Contacts for 2VSM CSU: Contacts of Structural Units for 2VSM Likely Quarternary Molecular Structure file(s) for 2VSM Structure Factors (755 Kb) Retrieve 2VSM in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2VSM from S2C, [Save to disk] Re-refined 2vsm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2VSM 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 2VSM

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 2VSM, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2vsm_A] [2vsm_B] [2vsm] SWISS-PROT database: [P52799] [Q9IH62] Domain organization of [EFNB2_HUMAN] [GLYCP_NIPAV] by SWISSPFAM

Other resources with information on 2VSM

Community annotation for 2VSM at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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