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Yorodumi- PDB-1vbt: Structure of cyclophilin complexed with sulfur-substituted tetrap... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vbt | ||||||
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Title | Structure of cyclophilin complexed with sulfur-substituted tetrapeptide AAPF | ||||||
Components |
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Keywords | ISOMERASE/ISOMERASE SUBSTRATE / CYCLOPHILIN A / PEPTIDYL-PROLYL ISOMERASE / COMPETITIVE INHIBITOR / ISOMERASE-ISOMERASE SUBSTRATE COMPLEX | ||||||
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 / virion binding / leukocyte chemotaxis / endothelial cell activation ...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 / 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 / protein peptidyl-prolyl isomerization / Calcineurin activates NFAT / viral release from host cell / 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 / 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 / platelet aggregation / integrin binding / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein 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 / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Zhao, Y. / Chen, Y. / Schutkowski, M. / Fischer, G. / Ke, H. | ||||||
Citation | Journal: To be Published Title: Insight Into Conversion of Substrate to Inhibitor Authors: Zhao, Y. / Chen, Y. / Schutkowski, M. / Fischer, G. / Ke, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vbt.cif.gz | 91.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vbt.ent.gz | 70.6 KB | Display | PDB format |
PDBx/mmJSON format | 1vbt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vbt_validation.pdf.gz | 379.9 KB | Display | wwPDB validaton report |
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Full document | 1vbt_full_validation.pdf.gz | 381.8 KB | Display | |
Data in XML | 1vbt_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 1vbt_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/1vbt ftp://data.pdbj.org/pub/pdb/validation_reports/vb/1vbt | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-1, -0.017, 0.007), Vector: |
-Components
#1: Protein | Mass: 18036.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: XA-90 F' / Gene: CYCLOPHILIN / Cell line (production host): XA-90 F' / Gene (production host): CYCLOPHILIN / Production host: Escherichia coli (E. coli) / References: UniProt: P05092, UniProt: P62937*PLUS #2: Protein/peptide | Mass: 540.634 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SYNTHETIC PEPTIDE #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.4 % |
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Crystal grow | pH: 8.2 / Details: pH 8.2 |
-Data collection
Diffraction | Mean temperature: 174 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 16964 / % possible obs: 80 % / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 |
Reflection shell | Resolution: 2.3→2.4 Å / % possible all: 46 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: UNLIGATED CYCLOPHILIN A Resolution: 2.3→10 Å / σ(F): 1
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Displacement parameters | Biso mean: 26.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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Refine LS restraints |
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