3EYF	Immune System	date	Oct 20, 2008
title	Crystal Structure Of Anti-Human Cytomegalovirus Antibody 8f9 Peptide
authors	C.A.Thomson, S.Bryson, G.R.Mclean, A.L.Creagh, E.F.Pai, J.W.Schra
compound		source
Molecule: 8f9 Fab Chain: A, C Engineered: Yes		Organism_scientific: Homo Sapiens Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet32b
Molecule: Ad-2 Chain: B, D Engineered: Yes		Organism_scientific: Homo Sapiens Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet40
Molecule: Synthetic Peptide Chain: E, F Engineered: Yes		Synthetic: Yes Other_details: Synthetic Peptide Following The Sequence Of 69-78 Of Glycoprotein B From Human Cytomegalovirus, Uniprot P13201 (Vglb_hcmvt)
symmetry	Space Group: P 21 21 21	R_factor 0.210 R_Free 0.230
crystal cell	length a length b length c angle alpha angle beta angle gamma 63.300 103.500 152.500 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.30 Å
ligand	GOL, NH2	enzyme
Primary reference	Germline V-genes sculpt the binding site of a family of antibodies neutralizing human cytomegalovirus., Thomson CA, Bryson S, McLean GR, Creagh AL, Pai EF, Schrader JW, EMBO J. 2008 Oct 8;27(19):2592-602. Epub 2008 Sep 4. PMID:18772881

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (148 Kb) [Save to disk] Biological Unit Coordinates (3eyf.pdb1.gz) 74 Kb Biological Unit Coordinates (3eyf.pdb2.gz) 72 Kb LPC: Ligand-Protein Contacts for 3EYF CSU: Contacts of Structural Units for 3EYF Likely Quarternary Molecular Structure file(s) for 3EYF Structure Factors (569 Kb) Retrieve 3EYF in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3EYF from S2C, [Save to disk] Re-refined 3eyf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3EYF 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 3EYF

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 3EYF, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3eyf_A] [3eyf_E] [3eyf_D] [3eyf_B] [3eyf_C] [3eyf_F] [3eyf] SWISS-PROT database: [P13201] [P01857] [P01834] Domain organization of [GB_HCMVT] [IGHG1_HUMAN] [IGKC_HUMAN] by SWISSPFAM Domains found in 3EYF: [IG_like] [IGv ] by SMART

Other resources with information on 3EYF

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

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