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Yorodumi- PDB-1cwc: IMPROVED BINDING AFFINITY FOR CYCLOPHILIN A BY A CYCLOSPORIN DERI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cwc | ||||||
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Title | IMPROVED BINDING AFFINITY FOR CYCLOPHILIN A BY A CYCLOSPORIN DERIVATIVE SINGLY MODIFIED AT ITS EFFECTOR DOMAIN | ||||||
Components |
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Keywords | ISOMERASE/IMMUNOSUPPRESSANT / ISOMERASE-IMMUNOSUPPRESSANT COMPLEX / CYCLOPHILIN-CYCLOSPORIN COMPLEX / CYCLOSPORIN A / IMMUNOSUPPRESSANT / CYCLOPHILIN | ||||||
Function / homology | Function and homology information negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / negative regulation of viral life cycle / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / endothelial cell activation ...negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / negative regulation of viral life cycle / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / endothelial cell activation / negative regulation of stress-activated MAPK cascade / Basigin interactions / cyclosporin A binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / viral release from host cell / protein peptidyl-prolyl isomerization / Calcineurin activates NFAT / Binding and entry of HIV virion / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / : / neutrophil chemotaxis / activation of protein kinase B activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of protein phosphorylation / platelet aggregation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of protein secretion / negative regulation of protein kinase activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / neuron differentiation / platelet activation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / integrin binding / Platelet degranulation / protein folding / positive regulation of NF-kappaB transcription factor activity / cellular response to oxidative stress / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / positive regulation of protein phosphorylation / intracellular membrane-bounded organelle / focal adhesion / Neutrophil degranulation / apoptotic process / protein-containing complex / RNA binding / extracellular space / extracellular exosome / extracellular region / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) TOLYPOCLADIUM INFLATUM (fungus) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.86 Å | ||||||
Authors | Mikol, V. | ||||||
Citation | Journal: J.Med.Chem. / Year: 1994 Title: Improved Binding Affinity for Cyclophilin a by a Cyclosporin Derivative Singly Modified at its Effector Domain. Authors: Papageorgiou, C. / Florineth, A. / Mikol, V. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1994 Title: Crystallization of the Complex between Cyclophilin a and Cyclosporin Derivatives: The Use of Cross- Seeding. Authors: Mikol, V. / Duc, D. #2: Journal: Protein Eng. / Year: 1994 Title: The X-Ray Structure of (Mebm2T)1-Cyclosporin Complexed with Cyclophilin a Provides an Explanation for its Anomalously High Immunosuppressive Activity. Authors: Mikol, V. / Kallen, J. / Walkinshaw, M.D. #3: Journal: J.Mol.Biol. / Year: 1993 Title: X-Ray Structure of a Monomeric Cyclophilin A- Cyclosporin a Crystal Complex at 2.1 A Resolution. Authors: Mikol, V. / Kallen, J. / Pflugl, G. / Walkinshaw, M.D. #4: Journal: Nature / Year: 1993 Title: X-Ray Structure of a Decameric Cyclophilin- Cyclosporin Crystal Complex. Authors: Pflugl, G. / Kallen, J. / Schirmer, T. / Jansonius, J.N. / Zurini, M.G. / Walkinshaw, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cwc.cif.gz | 52.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cwc.ent.gz | 36.7 KB | Display | PDB format |
PDBx/mmJSON format | 1cwc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cwc_validation.pdf.gz | 375.6 KB | Display | wwPDB validaton report |
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Full document | 1cwc_full_validation.pdf.gz | 377.5 KB | Display | |
Data in XML | 1cwc_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | 1cwc_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cw/1cwc ftp://data.pdbj.org/pub/pdb/validation_reports/cw/1cwc | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: VAL C 5 - LEU C 6 OMEGA = 359.98 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION |
-Components
#1: Protein | Mass: 18036.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Gene: CYCLOPHILIN / Gene (production host): CYCLOPHILIN / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P05092, UniProt: P62937*PLUS, peptidylprolyl isomerase |
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#2: Protein/peptide | Type: Cyclic peptide / Class: Immunosuppressant / Mass: 1234.652 Da / Num. of mol.: 1 / Mutation: YES / Source method: obtained synthetically Details: 4, N-DIMETHYLNORLEUCINE AT POSITION 8, CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI. THE CYCLOSPORIN MOLECULE WAS MODIFIED AT POSITION ...Details: 4, N-DIMETHYLNORLEUCINE AT POSITION 8, CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI. THE CYCLOSPORIN MOLECULE WAS MODIFIED AT POSITION 8 TO BE 4,N-DIMETHYLNORLEUCINE. Source: (synth.) TOLYPOCLADIUM INFLATUM (fungus) References: NOR: NOR00033, Cyclosporin A variant, MLE 8 to MNL |
#3: Water | ChemComp-HOH / |
Compound details | CYCLOSPORI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.89 % |
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Crystal grow | *PLUS Method: unknown |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.86→10 Å / Num. obs: 12126 / % possible obs: 86.2 % / Observed criterion σ(I): 2 |
-Processing
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Refinement | Resolution: 1.86→8 Å / Rfactor Rwork: 0.177 / Rfactor obs: 0.177 / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→8 Å
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