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- PDB-9upk: Entamoeba histolytica Cyclophilin 18 in complex with Alisporivir -

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Basic information

Entry
Database: PDB / ID: 9upk
TitleEntamoeba histolytica Cyclophilin 18 in complex with Alisporivir
Components
  • Alisporivir
  • Peptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / cyclophilin / PPIase
Function / homology
Function and homology information


cyclosporin A binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
ACETATE ION / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesEntamoeba histolytica HM-1:IMSS (eukaryote)
Tolypocladium inflatum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGandhi, S. / Vasudevan, D.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: To Be Published
Title: Crystal structure of Entamoeba histolytica cyclophilin 18 in complex with Alisporivir
Authors: Gandhi, S. / Vasudevan, D.
History
DepositionApr 28, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2026Provider: repository / Type: Initial release

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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
B: Peptidyl-prolyl cis-trans isomerase
C: Alisporivir
D: Alisporivir
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9918
Polymers38,7554
Non-polymers2364
Water4,035224
1
A: Peptidyl-prolyl cis-trans isomerase
C: Alisporivir
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4373
Polymers19,3782
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-9 kcal/mol
Surface area7990 Å2
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase
D: Alisporivir
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5555
Polymers19,3782
Non-polymers1773
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-10 kcal/mol
Surface area7830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.381, 85.855, 62.878
Angle α, β, γ (deg.)90.00, 104.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase / PPIase


Mass: 18144.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica HM-1:IMSS (eukaryote)
Gene: EHI7A_066540 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LEMO21 / References: UniProt: N9TCE9, peptidylprolyl isomerase
#2: Protein/peptide Alisporivir


Mass: 1232.637 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Tolypocladium inflatum (fungus)
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.55 Å3/Da / Density % sol: 51.72 % / Description: Rod Shaped
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 20% v/v 2-Propanol, 20% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.967 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 1.6→49.7 Å / Num. obs: 50234 / % possible obs: 99 % / Redundancy: 5.2 % / CC1/2: 0.99 / Net I/σ(I): 9.3
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 3.9 / Num. unique obs: 2553 / CC1/2: 0.913 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→49.7 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1862 2401 4.78 %
Rwork0.1662 --
obs0.1672 50192 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→49.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2714 0 16 224 2954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092780
X-RAY DIFFRACTIONf_angle_d1.1353746
X-RAY DIFFRACTIONf_dihedral_angle_d13.469382
X-RAY DIFFRACTIONf_chiral_restr0.065404
X-RAY DIFFRACTIONf_plane_restr0.009494
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.18931350.18352877X-RAY DIFFRACTION100
1.63-1.670.20921320.17952809X-RAY DIFFRACTION100
1.67-1.710.19881460.16982869X-RAY DIFFRACTION100
1.71-1.750.19551620.17542772X-RAY DIFFRACTION100
1.75-1.80.22931510.18632828X-RAY DIFFRACTION100
1.8-1.850.21291320.19172829X-RAY DIFFRACTION100
1.85-1.910.20821470.17492813X-RAY DIFFRACTION100
1.91-1.980.19481420.16752801X-RAY DIFFRACTION99
1.98-2.060.19291350.17172784X-RAY DIFFRACTION99
2.06-2.150.19861450.17192804X-RAY DIFFRACTION99
2.15-2.260.17061310.16222786X-RAY DIFFRACTION98
2.26-2.410.18791090.16142675X-RAY DIFFRACTION93
2.41-2.590.18621340.16572724X-RAY DIFFRACTION96
2.59-2.850.19691530.17232837X-RAY DIFFRACTION100
2.85-3.270.22961290.18072857X-RAY DIFFRACTION100
3.27-4.110.17331390.15532868X-RAY DIFFRACTION100
4.11-49.70.14861790.14542858X-RAY DIFFRACTION100

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