9LS5 | pdb_00009ls5

Entamoeba histolytica Cyclophilin 18 (apo)

PDB DOI: https://doi.org/10.2210/pdb9LS5/pdb

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

Deposited: 2025-02-03 Released: 2026-02-11
Deposition Author(s): Gandhi, S., Vasudevan, D.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.190 (Depositor), 0.190 (DCC)
R-Value Work:
0.159 (Depositor), 0.159 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Entamoeba histolytica cyclophilin 18

Gandhi, S., Vasudevan, D.

To be published.

Macromolecule Content

Total Structure Weight: 38.59 kDa
Atom Count: 2,753
Modeled Residue Count: 334
Deposited Residue Count: 350
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase	A, B	175	Entamoeba histolytica HM-1:IMSS	Mutation(s): 0 Gene Names: EHI_125840 EC: 5.2.1.8
UniProt
Find proteins for A0A8U0WPD6 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)) Explore A0A8U0WPD6 Go to UniProtKB: A0A8U0WPD6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8U0WPD6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.190 (Depositor), 0.190 (DCC)
R-Value Work: 0.159 (Depositor), 0.159 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.401	α = 90
b = 74.077	β = 104.64
c = 62.813	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-02-11

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2026-02-11
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.