1YJD	Immune System Signaling Protein	date	Jan 14, 2005
title	Crystal Structure Of Human Cd28 In Complex With The Fab Frag Mitogenic Antibody (5.11a1)
authors	E.J.Evans, R.M.Esnouf, R.Manso-Sancho, R.J.C.Gilbert, J.R.James, P.Sorensen, D.I.Stuart, S.J.Davis
compound		source
Molecule: Fab Fragment Of 5.11a1 Antibody Light Chain Chain: L		Organism_scientific: Mus Musculus Organism_common: House Mouse Organism_taxid: 10090
Molecule: Fab Fragment Of 5.11a1 Antibody Heavy Chain Chain: H Fragment: Igv And Igc1 Domains		Organism_scientific: Mus Musculus Organism_common: House Mouse Organism_taxid: 10090
Molecule: T-Cell-Specific Surface Glycoprotein Cd28 Chain: C Fragment: Extracellular Region Synonym: Tp44 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Cd28 Expression_system: Cricetulus Griseus Expression_system_common: Chinese Hamster Expression_system_taxid: 10029 Expression_system_strain: Cho Lec3.2.8.1 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pee14
symmetry	Space Group: C 1 2 1	R_factor 0.239 R_Free 0.282
crystal cell	length a length b length c angle alpha angle beta angle gamma 191.219 47.417 71.842 90.00 94.45 90.00
method	X-Ray Diffraction	resolution	2.70 Å
ligand	NAG	enzyme
related structures	by homologous chain: 1HH9, 1HQ4, 1MCP
Gene Ontology	Chain Function Process Component C
Primary reference	Crystal structure of a soluble CD28-Fab complex., Evans EJ, Esnouf RM, Manso-Sancho R, Gilbert RJ, James JR, Yu C, Fennelly JA, Vowles C, Hanke T, Walse B, Hunig T, Sorensen P, Stuart DI, Davis SJ, Nat Immunol 2005 Mar;6(3):271-9. Epub 2005 Feb 6. PMID:15696168

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (95 Kb) [Save to disk] Biological Unit Coordinates (1yjd.pdb1.gz) 177 Kb LPC: Ligand-Protein Contacts for 1YJD CSU: Contacts of Structural Units for 1YJD Likely Quarternary Molecular Structure file(s) for 1YJD Structure Factors (140 Kb) Retrieve 1YJD in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1YJD from S2C, [Save to disk] Re-refined 1yjd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1YJD 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 1YJD

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 1YJD, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1yjd_C] [1yjd] [1yjd_H] [1yjd_L] SWISS-PROT database: [P10747] Domain organization of [CD28_HUMAN] by SWISSPFAM Domains found in 1YJD: [IG_like] [IGv ] by SMART

Other resources with information on 1YJD

Community annotation for 1YJD at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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