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- PDB-6gji: Cyclophilin A complexed with the tri-vector ligand 8. -

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Basic information

Entry
Database: PDB / ID: 6gji
TitleCyclophilin A complexed with the tri-vector ligand 8.
ComponentsPeptidyl-prolyl cis-trans isomerase A
KeywordsISOMERASE / Cyclophilins / CypA / inhibitor / PPIase / complex
Function / homology
Function and homology information


negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / negative regulation of viral life cycle / 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 / regulation of apoptotic signaling pathway / negative regulation of viral life cycle / 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 / 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 / peptidylprolyl isomerase / positive regulation of protein secretion / peptidyl-prolyl cis-trans isomerase activity / negative regulation of protein kinase activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / platelet activation / neuron differentiation / 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 / positive regulation of protein phosphorylation / focal adhesion / Neutrophil degranulation / apoptotic process / protein-containing complex / RNA binding / extracellular space / extracellular exosome / extracellular region / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-F1E / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGeorgiou, C. / De Simone, A. / Walkinshaw, M.D. / Michel, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research CouncilNo. 336289 United Kingdom
CitationJournal: Chem Sci / Year: 2019
Title: A computationally designed binding mode flip leads to a novel class of potent tri-vector cyclophilin inhibitors.
Authors: De Simone, A. / Georgiou, C. / Ioannidis, H. / Gupta, A.A. / Juarez-Jimenez, J. / Doughty-Shenton, D. / Blackburn, E.A. / Wear, M.A. / Richards, J.P. / Barlow, P.N. / Carragher, N. / ...Authors: De Simone, A. / Georgiou, C. / Ioannidis, H. / Gupta, A.A. / Juarez-Jimenez, J. / Doughty-Shenton, D. / Blackburn, E.A. / Wear, M.A. / Richards, J.P. / Barlow, P.N. / Carragher, N. / Walkinshaw, M.D. / Hulme, A.N. / Michel, J.
History
DepositionMay 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4753
Polymers18,0371
Non-polymers4382
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint1 kcal/mol
Surface area7620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.621, 54.535, 87.486
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase A / PPIase A / Cyclophilin A / Cyclosporin A-binding protein / Rotamase A


Mass: 18036.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIA, CYPA / Production host: Escherichia coli (E. coli) / References: UniProt: P62937, peptidylprolyl isomerase
#2: Chemical ChemComp-F1E / ethyl 2-[[(4-aminophenyl)methyl-[(1-methyl-1,2,3-triazol-4-yl)methyl]carbamoyl]amino]ethanoate


Mass: 346.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H22N6O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 279.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 8000, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.597→87.486 Å / Num. obs: 27755 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.043 / Rrim(I) all: 0.08 / Net I/σ(I): 13.5
Reflection shellResolution: 1.597→1.625 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1350 / CC1/2: 0.886 / Rpim(I) all: 0.366 / Rrim(I) all: 0.689 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NOY

5noy


Resolution: 1.6→46.28 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.776 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19071 1431 5.2 %RANDOM
Rwork0.15254 ---
obs0.15449 26324 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.126 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.01 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.6→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1266 0 31 225 1522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0191387
X-RAY DIFFRACTIONr_bond_other_d0.0020.021315
X-RAY DIFFRACTIONr_angle_refined_deg1.9961.9721861
X-RAY DIFFRACTIONr_angle_other_deg1.2633036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.225174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.1423.7761
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20615238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.812158
X-RAY DIFFRACTIONr_chiral_restr0.1440.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021592
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02338
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5822.467669
X-RAY DIFFRACTIONr_mcbond_other2.4792.455668
X-RAY DIFFRACTIONr_mcangle_it3.9493.669839
X-RAY DIFFRACTIONr_mcangle_other3.9983.681838
X-RAY DIFFRACTIONr_scbond_it3.8732.913718
X-RAY DIFFRACTIONr_scbond_other3.8662.913718
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.074.1911018
X-RAY DIFFRACTIONr_long_range_B_refined9.36422.2151601
X-RAY DIFFRACTIONr_long_range_B_other9.35122.2161601
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.597→1.638 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 107 -
Rwork0.248 1890 -
obs--99.95 %

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