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 Diffractionresolution 1.70 Å
ligand MES, ZN enzyme Isomerase E.C.5.2.1.8 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


C


Primary referenceStructural 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.
  • 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] [3ici_C] [3ici_B]
  • 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)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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