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Yorodumi- PDB-1mik: THE ROLE OF WATER MOLECULES IN THE STRUCTURE-BASED DESIGN OF (5-H... -
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-Basic information
Entry | Database: PDB / ID: 1mik | ||||||
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Title | THE ROLE OF WATER MOLECULES IN THE STRUCTURE-BASED DESIGN OF (5-HYDROXYNORVALINE)-2-CYCLOSPORIN: SYNTHESIS, BIOLOGICAL ACTIVITY, AND CRYSTALLOGRAPHIC ANALYSIS WITH CYCLOPHILIN A | ||||||
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 / 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 / Resolution: 1.76 Å | ||||||
Authors | Mikol, V. | ||||||
Citation | Journal: J.Med.Chem. / Year: 1995 Title: The Role of Water Molecules in the Structure-Based Design of (5-Hydroxynorvaline)-2-Cyclosporin: Synthesis, Biological Activity, and Crystallographic Analysis with Cyclophilin A. Authors: Mikol, V. / Papageorgiou, C. / Borer, X. #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: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mik.cif.gz | 52.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mik.ent.gz | 37.1 KB | Display | PDB format |
PDBx/mmJSON format | 1mik.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mik_validation.pdf.gz | 377.1 KB | Display | wwPDB validaton report |
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Full document | 1mik_full_validation.pdf.gz | 379.7 KB | Display | |
Data in XML | 1mik_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | 1mik_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/1mik ftp://data.pdbj.org/pub/pdb/validation_reports/mi/1mik | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 1250.651 Da / Num. of mol.: 1 / Mutation: YES / Source method: obtained synthetically Details: 2-AMINO-5-HYDROXYPENTANOIC ACID AT POSITION 6, CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI. THE CYCLOSPORIN A MOLECULE WAS MODIFIED AT ...Details: 2-AMINO-5-HYDROXYPENTANOIC ACID AT POSITION 6, CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI. THE CYCLOSPORIN A MOLECULE WAS MODIFIED AT POSITION 6 TO BE 2-AMINO-5-HYDROXYPENTANOIC ACID Source: (synth.) TOLYPOCLADIUM INFLATUM (fungus) / References: NOR: NOR00033, CYCLOSPORIN A, 6 mutation |
#3: Water | ChemComp-HOH / |
Compound details | CYCLOSPORI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.46 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 8.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.76→8 Å / Num. obs: 14501 / % possible obs: 87.2 % / Observed criterion σ(I): 2 |
Reflection | *PLUS Num. measured all: 46587 / Rmerge(I) obs: 0.043 |
-Processing
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Refinement | Resolution: 1.76→8 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 1.76→8 Å
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Refine LS restraints |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |