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Yorodumi- PDB-1cwk: HUMAN CYCLOPHILIN A COMPLEXED WITH 1-(6,7-DIHYDRO)MEBMT 2-VAL 3-D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cwk | ||||||
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Title | HUMAN CYCLOPHILIN A COMPLEXED WITH 1-(6,7-DIHYDRO)MEBMT 2-VAL 3-D-(2-S-METHYL)SARCOSINE CYCLOSPORIN | ||||||
Components |
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Keywords | ISOMERASE/IMMUNOSUPPRESSANT / ISOMERASE-IMMUNOSUPPRESSANT COMPLEX / CYCLOPHILIN-CYCLOSPORIN COMPLEX / CYCLOSPORIN D / IMMUNOSUPPRESSANT / CYCLOPHILIN | ||||||
Function / homology | Function and homology information negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / endothelial cell activation / virion binding ...negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / endothelial cell activation / virion binding / Basigin interactions / negative regulation of stress-activated MAPK cascade / 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 / Calcineurin activates NFAT / viral release from host cell / Binding and entry of HIV virion / positive regulation of viral genome replication / protein peptidyl-prolyl isomerization / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of protein dephosphorylation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / activation of protein kinase B activity / neutrophil chemotaxis / negative regulation of protein phosphorylation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of protein secretion / Assembly Of The HIV Virion / negative regulation of protein kinase activity / Budding and maturation of HIV virion / neuron differentiation / platelet activation / platelet aggregation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / integrin binding / protein folding / Platelet degranulation / 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 / response to hypoxia / positive regulation of protein phosphorylation / intracellular membrane-bounded organelle / focal adhesion / apoptotic process / Neutrophil degranulation / protein-containing complex / RNA binding / extracellular space / extracellular exosome / extracellular region / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) TOLYPOCLADIUM INFLATUM (fungus) | ||||||
Method | X-RAY DIFFRACTION / PROTEIN STRUCTURE KNOWN IN THIS CELL / Resolution: 1.8 Å | ||||||
Authors | Mikol, V. / Kallen, J. / Taylor, P. / Walkinshaw, M.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: X-Ray Structures and Analysis of 11 Cyclosporin Derivatives Complexed with Cyclophilin A. Authors: Kallen, J. / Mikol, V. / Taylor, P. / 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 | 1cwk.cif.gz | 48 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cwk.ent.gz | 36.3 KB | Display | PDB format |
PDBx/mmJSON format | 1cwk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cwk_validation.pdf.gz | 380.3 KB | Display | wwPDB validaton report |
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Full document | 1cwk_full_validation.pdf.gz | 381.6 KB | Display | |
Data in XML | 1cwk_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | 1cwk_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cw/1cwk ftp://data.pdbj.org/pub/pdb/validation_reports/cw/1cwk | HTTPS FTP |
-Related structure data
Related structure data | 1bckC 1cwfSC 1cwhC 1cwiC 1cwjC 1cwlC 1cwmC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-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: 1282.759 Da / Num. of mol.: 1 / Mutation: YES / Source method: obtained synthetically Details: (2-S-METHYL) SARCOSINE AT POSITION 7,(6,7-DIHYDRO)4-[(E)-BUTENYL]-4, N-DIMETHYL-THREONINE AT POSITION 5, CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND ...Details: (2-S-METHYL) SARCOSINE AT POSITION 7,(6,7-DIHYDRO)4-[(E)-BUTENYL]-4, N-DIMETHYL-THREONINE AT POSITION 5, CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI. CYCLOSPORIN D IS A NATURAL ANALOG OF CYCLOSPORIN A, OBTAINED IN DIFFERENT NUTRIENT BROTH AND DIFFERS FROM CYCLOSPORIN IN RESIDUE 6 (ABA6VAL). THE CYCLOSPORIN D MOLECULE WAS MODIFIED AT POSITIONS 5 AND 7 TO BE (6,7-DIHYDRO)4-[(E)-BUTENYL]-4,N-DIMETHYL-THREONINE AND (2-S-METHYL)-SARCOSINE, RESPECTIVELY. Source: (synth.) TOLYPOCLADIUM INFLATUM (fungus) / References: NOR: NOR00036, CYCLOSPORIN D, 5,7 mutation |
#3: Water | ChemComp-HOH / |
Compound details | CYCLOSPORI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 41 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: PH 8.0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 295 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS / Detector: AREA DETECTOR / Date: Jun 1, 1993 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.8 Å / Num. obs: 14288 / % possible obs: 92.3 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rsym value: 0.058 |
Reflection | *PLUS Num. measured all: 45753 / Rmerge(I) obs: 0.058 |
-Processing
Software |
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Refinement | Method to determine structure: PROTEIN STRUCTURE KNOWN IN THIS CELL Starting model: PDB ENTRY 1CWF Resolution: 1.8→8 Å / Data cutoff high absF: 30000 / Data cutoff low absF: 0.1 / σ(F): 2
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Displacement parameters | Biso mean: 18.87 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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Refine LS restraints |
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Xplor file |
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