3ICI	Isomerase	date	Jul 17, 2009
title	Crystal Structure Of Cyclophilin B In Complex With Calmegin
authors	G.Kozlov, K.Gehring
compound		source
Molecule: Peptidyl-Prolyl Cis-Trans Isomerase B Chain: A, B Fragment: Unp Residues 34-216 Synonym: Ppiase, Rotamase, Cyclophilin B, S-Cyclophilin, Sc S1; Ec: 5.2.1.8 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ppib, Cypb Expression_system: Escherichia Coli Expression_system_taxid: 511693 Expression_system_strain: Bl21 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pgex-6p-1
Molecule: Calnexin Chain: C Fragment: P-Domain Fragment: Residues 317-350 Synonym: Pp90 Engineered: Yes		Organism_scientific: Canis Lupus Familiaris Organism_common: Dog Organism_taxid: 9615 Gene: Canx Expression_system: Escherichia Coli Expression_system_taxid: 511693 Expression_system_strain: Bl21 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet15b
symmetry	Space Group: P 1	R_factor 0.188 R_Free 0.239
crystal cell	length a length b length c angle alpha angle beta angle gamma 43.411 44.295 55.427 89.94 94.46 114.03
method	X-Ray Diffraction	resolution	1.70 Å
ligand	MES, ZN	enzyme	Isomerase E.C.5.2.1.8 BRENDA
Gene Ontology	Chain Function Process Component A, B peptidyl-prolyl cis-trans is... protein binding isomerase activity peptide binding unfolded protein binding protein peptidyl-prolyl isom... protein folding extracellular matrix organiz... endoplasmic reticulum endoplasmic reticulum lumen melanosome
Primary reference	Structural basis of cyclophilin B binding by the calnexin/calreticulin P-domain., Kozlov G, Bastos-Aristizabal S, Maattanen P, Rosenauer A, Zheng F, Killikelly A, Trempe JF, Thomas DY, Gehring K, J Biol Chem. 2010 Sep 3. PMID:20801878

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (76 Kb) [Save to disk] Biological Unit Coordinates (3ici.pdb1.gz) 37 Kb Biological Unit Coordinates (3ici.pdb2.gz) 36 Kb LPC: Ligand-Protein Contacts for 3ICI CSU: Contacts of Structural Units for 3ICI Structure Factors (591 Kb) Retrieve 3ICI in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3ICI from S2C, [Save to disk] Re-refined 3ici structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3ICI 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 3ICI

Cartoon representation from PDB Cartoon 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 Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 3ICI, from MSDmotif at EBI Fold representative 3ici from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3ici_A] [3ici_B] [3ici_C] SWISS-PROT database: Domain organization of by SWISSPFAM Alignments of the sequence of 3ICI with the sequences similar proteins can be viewed for 3ICI's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.

Other resources with information on 3ICI

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

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