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- PDB-9upj: Entamoeba histolytica Cyclophilin 18 in complex with Voclosporin -

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Basic information

Entry
Database: PDB / ID: 9upj
TitleEntamoeba histolytica Cyclophilin 18 in complex with Voclosporin
Components
  • Peptidyl-prolyl cis-trans isomerase
  • Voclosporin
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
ISOPROPYL ALCOHOL / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesEntamoeba histolytica HM-1:IMSS (eukaryote)
Tolypocladium inflatum (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 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

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase
B: Peptidyl-prolyl cis-trans isomerase
C: Voclosporin
D: Voclosporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0546
Polymers40,9334
Non-polymers1202
Water3,279182
1
A: Peptidyl-prolyl cis-trans isomerase
C: Voclosporin


Theoretical massNumber of molelcules
Total (without water)20,4672
Polymers20,4672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-5 kcal/mol
Surface area8000 Å2
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase
D: Voclosporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5874
Polymers20,4672
Non-polymers1202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-6 kcal/mol
Surface area7990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.858, 85.571, 62.653
Angle α, β, γ (deg.)90.00, 104.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 19234.076 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 Voclosporin


Mass: 1232.635 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Tolypocladium inflatum (fungus)
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 18% v/v 2-Propanol, 0.1 M Sodium citrate tribasic dihydrate pH 5.5, 20% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jun 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.5→30.37 Å / Num. obs: 60182 / % possible obs: 100 % / Redundancy: 5.4 % / CC1/2: 0.998 / Net I/σ(I): 12
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2977 / CC1/2: 0.871 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→30.37 Å / SU B: 2.609 / SU ML: 0.043 / Cross valid method: FREE R-VALUE / ESU R: 0.073 / ESU R Free: 0.064 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1851 3030 5 %RANDOM
Rwork0.15722 ---
obs0.15863 57125 99.95 %-
Displacement parametersBiso mean: 9.159 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20.08 Å2
2---0.21 Å20 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2716 0 8 182 2906
LS refinement shellResolution: 1.5→1.52 Å
RfactorNum. reflection% reflection
Rfree0.24 150 -
Rwork0.21 2566 -
obs--99.67 %

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