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- PDB-6gs6: Cyclophilin A single mutant D66A in complex with an inhibitor. -

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Basic information

Entry
Database: PDB / ID: 6gs6
TitleCyclophilin A single mutant D66A in complex with an inhibitor.
ComponentsPeptidyl-prolyl cis-trans isomerase A
KeywordsISOMERASE / Cyclophilins / CypA / CypA mutant / inhibitor / PPIase / complex
Function / homology
Function and homology information


negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade ...negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / endothelial cell activation / protein peptidyl-prolyl isomerization / Basigin interactions / cyclosporin A binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / Early Phase of HIV Life Cycle / Integration of provirus / negative regulation of protein phosphorylation / APOBEC3G mediated resistance to HIV-1 infection / viral release from host cell / Calcineurin activates NFAT / activation of protein kinase B activity / Binding and entry of HIV virion / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / neutrophil chemotaxis / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of protein secretion / peptidyl-prolyl cis-trans isomerase activity / peptidylprolyl isomerase / Assembly Of The HIV Virion / positive regulation of NF-kappaB transcription factor activity / Budding and maturation of HIV virion / platelet activation / platelet aggregation / neuron differentiation / SARS-CoV-1 activates/modulates innate immune responses / integrin binding / unfolded protein binding / positive regulation of protein phosphorylation / Platelet degranulation / protein folding / cellular response to oxidative stress / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / focal adhesion / apoptotic process / Neutrophil degranulation / protein-containing complex / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleus / membrane / 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
ethyl N-[(4-aminobenzyl)carbamoyl]glycinate / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsGeorgiou, C. / De Simone, A. / Juarez-Jimenez, J. / Walkinshaw, M.D. / Michel, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research CouncilNo. 336289 United Kingdom
CitationJournal: Chem Sci / Year: 2020
Title: Dynamic design: manipulation of millisecond timescale motions on the energy landscape of cyclophilin A
Authors: Juarez-Jimenez, J. / Gupta, A.A. / Karunanithy, G. / May, A. / Georgiou, C. / Ioannidis, H. / De Simone, A. / Barlow, P.N. / Hulme, A.N. / Walkinshaw, M.D. / Baldwin, A. / Michel, J.
History
DepositionJun 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,3223
Polymers17,9921
Non-polymers3292
Water3,495194
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint2 kcal/mol
Surface area7700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.010, 63.010, 94.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-489-

HOH

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Components

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


Mass: 17992.494 Da / Num. of mol.: 1 / Mutation: D66A
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-EA4 / ethyl N-[(4-aminobenzyl)carbamoyl]glycinate


Mass: 251.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17N3O3
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 3.01 Å3/Da / Density % sol: 59.13 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 2.2 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.16→47.28 Å / Num. obs: 75550 / % possible obs: 99.64 % / Redundancy: 9.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.017 / Net I/σ(I): 14.2
Reflection shellResolution: 1.16→1.18 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1 / Num. unique obs: 3671 / CC1/2: 0.704 / Rpim(I) all: 0.723 / % possible all: 99.27

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
xia2data reduction
pointlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RDD

3rdd


Resolution: 1.16→47.28 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.481 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.029 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1699 3921 5.2 %RANDOM
Rwork0.1497 ---
obs0.15075 71625 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.891 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.26 Å20 Å2
2--0.51 Å2-0 Å2
3----1.66 Å2
Refinement stepCycle: 1 / Resolution: 1.16→47.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1222 0 22 194 1438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191342
X-RAY DIFFRACTIONr_bond_other_d0.0020.021279
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.9661798
X-RAY DIFFRACTIONr_angle_other_deg0.9232965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0445172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.82524.65558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16815239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.193155
X-RAY DIFFRACTIONr_chiral_restr0.0810.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021547
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02320
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_it3.0912.465674
X-RAY DIFFRACTIONr_mcbond_other3.0882.464675
X-RAY DIFFRACTIONr_mcangle_it4.1973.713847
X-RAY DIFFRACTIONr_mcangle_other4.1983.714847
X-RAY DIFFRACTIONr_scbond_it2.082.763668
X-RAY DIFFRACTIONr_scbond_other2.0792.767669
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.444950
X-RAY DIFFRACTIONr_long_range_B_refined4.49220.6741378
X-RAY DIFFRACTIONr_long_range_B_other4.49120.6991379
X-RAY DIFFRACTIONr_rigid_bond_restr1.19432621
X-RAY DIFFRACTIONr_sphericity_free31.4195127
X-RAY DIFFRACTIONr_sphericity_bonded16.53752657
LS refinement shellResolution: 1.16→1.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 283 -
Rwork0.312 5214 -
obs--99.17 %

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