8J7C

Crystal structure of triosephosphate isomerase from Leishmania orientalis at 1.88A with an arsenic ion bound at Cys57

PDB DOI: https://doi.org/10.2210/pdb8J7C/pdb
Entry: 8J7C supersedes: 5CG7

Classification: ISOMERASE
Organism(s): Leishmania orientalis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-04-27 Released: 2024-05-01
Deposition Author(s): Kuaprasert, B., Attarataya, J., Riangrungroj, P., Pornthanakasem, W., Suginta, W., Mungthin, M., Leelayoova, S., Choowongkomon, K., Leartsakulpanich, U.
Funding Organization(s): Synchrotron Light Research Institute (SLRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.214
R-Value Work: 0.171
R-Value Observed: 0.174

wwPDB Validation 3D Report Full Report

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

Literature

Leishmania orientalis triosephosphate isomerase crystal structure at 1.45 angstroms resolution and its potential specific inhibitors

Kuaprasert, B., Leartsakulpanich, U., Riangrungroj, P., Pornthanakasem, W., Suginta, W., Robinson, R., Zhou, Y., Mungthin, M., Leelayoova, S., Saehlee, S., Kiriwan, D., Choowongkomon, K.

To be published.

Macromolecule Content

Total Structure Weight: 58.64 kDa
Atom Count: 4,245
Modelled Residue Count: 488
Deposited Residue Count: 542
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Triosephosphate isomerase	A, B	271	Leishmania orientalis	Mutation(s): 0 Gene Names: LSCM4_05371 EC: 5.3.1.1
UniProt
Find proteins for A0A836H5J0 (Leishmania orientalis) Explore A0A836H5J0 Go to UniProtKB: A0A836H5J0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A836H5J0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ARS Query on ARS 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]	C [auth A], D [auth B]	ARSENIC As RBFQJDQYXXHULB-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: 1.88 Å
R-Value Free: 0.214
R-Value Work: 0.171
R-Value Observed: 0.174
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.44	α = 90
b = 76.45	β = 101.14
c = 94.94	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
pointless	data scaling
MOSFLM	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-01

Deposition Author(s):

Riangrungroj, P.

Pornthanakasem, W.

Choowongkomon, K.

Leartsakulpanich, U.

This entry supersedes: 5CG7

Funding Organization	Location	Grant Number
Synchrotron Light Research Institute (SLRI)	Thailand	--

Revision History (Full details and data files)

Version 1.0: 2024-05-01
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 R01GM133198.