9UPK | pdb_00009upk

Entamoeba histolytica Cyclophilin 18 in complex with Alisporivir

PDB DOI: https://doi.org/10.2210/pdb9UPK/pdb

Classification: ISOMERASE
Organism(s): Entamoeba histolytica HM-1:IMSS, Tolypocladium inflatum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-04-28 Released: 2026-05-20
Deposition Author(s): Gandhi, S., Vasudevan, D.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.186 (Depositor), 0.185 (DCC)
R-Value Work:
0.166 (Depositor), 0.165 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of Entamoeba histolytica cyclophilin 18 in complex with Alisporivir

Gandhi, S., Vasudevan, D.

To be published.

Macromolecule Content

Total Structure Weight: 38.99 kDa
Atom Count: 2,954
Modeled Residue Count: 356
Deposited Residue Count: 356
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase	A, B	167	Entamoeba histolytica HM-1:IMSS	Mutation(s): 0 Gene Names: EHI7A_066540 EC: 5.2.1.8
UniProt
Find proteins for N9TCE9 (Entamoeba histolytica HM-1:IMSS-A) Explore N9TCE9 Go to UniProtKB: N9TCE9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	N9TCE9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Alisporivir	C, D	11	Tolypocladium inflatum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth B], H [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B]

Modified Residues 5 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
DAM Query on DAM	C, D	ALA	Dehydroamino acid	C₄ H₇ N O₂
DAM Query on DAM	C, D	ALA	Methylation	C₄ H₇ N O₂
66E Query on 66E	C, D	VAL	Ethylation	C₇ H₁₅ N O₂
MLE Query on MLE	C, D	LEU	Methylation	C₇ H₁₅ N O₂
MVA Query on MVA	C, D	VAL	Methylation	C₆ H₁₃ N O₂

Non-standard Monomers 3 Unique
ID	Chains	Type	Formula	2D Diagram
ABA Query on ABA	C, D	L-PEPTIDE LINKING	C₄ H₉ N O₂
BMT Query on BMT	C, D	L-PEPTIDE LINKING	C₁₀ H₁₉ N O₃
DAL Query on DAL	C, D	D-PEPTIDE LINKING	C₃ H₇ N O₂

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.186 (Depositor), 0.185 (DCC)
R-Value Work: 0.166 (Depositor), 0.165 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.381	α = 90
b = 85.855	β = 104.25
c = 62.878	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	--

Revision History (Full details and data files)

Version 1.0: 2026-05-20
Type: Initial release