1RD9	Toxin	date	Nov 05, 2003
title	Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand Bv2
authors	J.C.Pickens, D.D.Mitchell, J.Liu, X.Tan, Z.Zhang, C.L.Verlinde, W.G.Hol, E.Fan
compound		source
Molecule: Cholera Toxin B Protein (Ctb) Chain: D, E, F, G, H Engineered: Yes		Organism_scientific: Vibrio Cholerae Organism_common: Bacteria Gene: Ctxb Expression_system: Escherichia Coli Expression_system_common: Bacteria Expression_system_strain: Top10 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pbad
symmetry	Space Group: C 1 2 1	R_factor	0.131
crystal cell	length a length b length c angle alpha angle beta angle gamma 101.983 66.072 77.818 90.00 105.84 90.00
method	X-Ray Diffraction	resolution	1.44 Å
ligand	BV2, P6G, TMN	enzyme
similarity	Belongs to the Enterotoxin_b family.
subunit	The a subunit contains two chains, a1 and a2, linked by a disulfide bridge. The holotoxin (choleragen) consists of a pentameric ring of b subunits whose central pore is occupied by the a subunit.
gene	ctxB (V. cholerae)
function	It can bind five gm1 gangliosides. The b subunit pentameric ring directs the a subunit to its target by binding to the gm1 gangliosides present on the surface of the intestinal epithelial cells. It has no toxic activity by itself.
Gene Ontology	Chain Function Process Component H, F, D, G, E pathogenesis extracellular region membrane
Primary reference	Nonspanning bivalent ligands as improved surface receptor binding inhibitors of the cholera toxin B pentamer., Pickens JC, Mitchell DD, Liu J, Tan X, Zhang Z, Verlinde CL, Hol WG, Fan E, Chem Biol 2004 Sep;11(9):1205-15. PMID:15380181

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (218 Kb) [Save to disk] Biological Unit Coordinates (1rd9.pdb1.gz) 192 Kb CSU: Contacts of Structural Units for 1RD9 Likely Quarternary Molecular Structure file(s) for 1RD9 Structure Factors (841 Kb) Retrieve 1RD9 in mmCIF format [Save to disk]

View 1RD9 in 3D

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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 1RD9

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Structure-derived information

Conformational Epitope Prediction for 1RD9 1RD9D 1RD9E 1RD9F 1RD9G 1RD9H from the CEP Server. Dipole moment, from Dipole Server at Weizmann Institute Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 1RD9, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1rd9d_, region D [Jmol] [rasmolscript] [script source]     - Domain d1rd9e_, region E [Jmol] [rasmolscript] [script source]     - Domain d1rd9f_, region F [Jmol] [rasmolscript] [script source]     - Domain d1rd9g_, region G [Jmol] [rasmolscript] [script source]     - Domain d1rd9h_, region H [Jmol] [rasmolscript] [script source] Fold representative 1rd9 from FSSP and Dali (Families of Structurally Similar Proteins) Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1rd9_D] [1rd9_F] [1rd9_H] [1rd9_G] [1rd9_E]

Other resources with information on 1RD9

InterPro: IPR001835 MMDB (Entrez's Structure Database)

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