2Y8D	Membrane Protein	date	Feb 04, 2011
title	Structure Of Dbl6 Epsilon Domain From Var2csa Strain Fcr3
authors	S.Gangnard, S.Ramboarina, A.Lewit-Bentley, G.A.Bentley
compound		source
Molecule: Erythrocyte Membrane Protein 1 Chain: A Fragment: Dbl6 Epsilon, Residues 2326-2631 Engineered: Yes		Organism_scientific: Plasmodium Falciparum Organism_taxid: 5833 Strain: Fcr3 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Shuffle Expression_system_vector_type: Plasmid Expression_system_vector: Pet15b
symmetry	Space Group: C 1 2 1	R_factor 0.203 R_Free 0.235
crystal cell	length a length b length c angle alpha angle beta angle gamma 85.859 56.229 75.849 90.00 123.09 90.00
method	X-Ray Diffraction	resolution	1.84 Å
ligand	BEN, DHL	enzyme
note	2Y8D is a representative structure
Gene Ontology	Chain Function Process Component A
Primary reference	Structural and Immunological Correlations between the Variable Blocks of the VAR2CSA Domain DBL6epsilon from Two Plasmodium falciparum Parasite Lines., Gangnard S, Badaut C, Ramboarina S, Baron B, Ramdani T, Gamain B, Deloron P, Lewit-Bentley A, Bentley GA, J Mol Biol. 2013 Feb 18. pii: S0022-2836(13)00100-9. doi:, 10.1016/j.jmb.2013.02.014. PMID:23429057

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (55 Kb) [Save to disk] Biological Unit Coordinates (2y8d.pdb1.gz) 50 Kb LPC: Ligand-Protein Contacts for 2Y8D CSU: Contacts of Structural Units for 2Y8D Structure Factors (561 Kb) Retrieve 2Y8D in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2Y8D from S2C, [Save to disk] Re-refined 2y8d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2Y8D 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 2Y8D

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 2Y8D, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2y8d_A] [2y8d] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 2Y8D

Community annotation for 2Y8D at PDBWiki (http://pdbwiki.org)

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