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- PDB-3rdd: Human Cyclophilin A Complexed with an Inhibitor -

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Basic information

Entry
Database: PDB / ID: 3rdd
TitleHuman Cyclophilin A Complexed with an Inhibitor
ComponentsPeptidyl-prolyl cis-trans isomerase A
KeywordsISOMERASE/ISOMERASE INHIBITOR / beta barrel / prolyl cis/trans isomerase / cytosolic / inhibitor / ISOMERASE-ISOMERASE INHIBITOR 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 / leukocyte chemotaxis / virion binding / 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 / leukocyte chemotaxis / virion binding / negative regulation of stress-activated MAPK cascade / endothelial cell activation / Basigin interactions / protein peptidyl-prolyl isomerization / 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 / 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 / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Assembly Of The HIV Virion / positive regulation of NF-kappaB transcription factor activity / Budding and maturation of HIV virion / platelet activation / platelet aggregation / integrin binding / positive regulation of protein phosphorylation / neuron differentiation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / 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 / cytoplasm / cytosol
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: 2.14 Å
AuthorsColliandre, L. / Ahmed-Belkacem, H. / Bessin, Y. / Pawlotsky, J.M. / Guichou, J.F.
CitationJournal: Nat Commun / Year: 2016
Title: Fragment-based discovery of a new family of non-peptidic small-molecule cyclophilin inhibitors with potent antiviral activities.
Authors: Ahmed-Belkacem, A. / Colliandre, L. / Ahnou, N. / Nevers, Q. / Gelin, M. / Bessin, Y. / Brillet, R. / Cala, O. / Douguet, D. / Bourguet, W. / Krimm, I. / Pawlotsky, J.M. / Guichou, J.F.
History
DepositionApr 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)20,5452
Polymers20,2941
Non-polymers2511
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.774, 52.377, 86.965
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 / Cyclophilin A / PPIase A / Cyclosporin A-binding protein / Rotamase A


Mass: 20293.943 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-EA4 / ethyl N-[(4-aminobenzyl)carbamoyl]glycinate


Mass: 251.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17N3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.29 Å3/Da / Density % sol: 46.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES, 20% PEG10000, 5% ethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 18, 2009
RadiationMonochromator: yale mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.14→35 Å / Num. all: 10210 / Num. obs: 10078 / % possible obs: 98.7 % / Observed criterion σ(I): 11.3 / Redundancy: 2.5 % / Rsym value: 0.057
Reflection shellResolution: 2.14→2.195 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.2 / Rsym value: 0.494 / % possible all: 97.2

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Processing

Software
NameVersionClassification
DNAdata collection
X-PLORmodel building
REFMAC5.4.0062refinement
MOSFLMdata reduction
SCALAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CYH

2cyh


Resolution: 2.14→33.46 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.502 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27165 509 4.8 %RANDOM
Rwork0.21561 ---
obs0.21829 10078 98.26 %-
all-10210 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.128 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20 Å20 Å2
2--1.97 Å20 Å2
3----3.56 Å2
Refinement stepCycle: LAST / Resolution: 2.14→33.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1249 0 18 90 1357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221295
X-RAY DIFFRACTIONr_bond_other_d0.0010.02902
X-RAY DIFFRACTIONr_angle_refined_deg1.231.9531736
X-RAY DIFFRACTIONr_angle_other_deg0.833.0032173
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4875163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7324.13858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.7115214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.579156
X-RAY DIFFRACTIONr_chiral_restr0.0770.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211474
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02279
X-RAY DIFFRACTIONr_mcbond_it0.5011.5807
X-RAY DIFFRACTIONr_mcbond_other0.0821.5347
X-RAY DIFFRACTIONr_mcangle_it0.94921286
X-RAY DIFFRACTIONr_scbond_it1.1293488
X-RAY DIFFRACTIONr_scangle_it1.8254.5450
LS refinement shellResolution: 2.14→2.195 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.462 34 -
Rwork0.328 704 -
obs--95.84 %

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