8JBP | pdb_00008jbp

Crystal structure of triosephosphate isomerase from Leishmania orientalis at 1.45 angstroms resolution with an arsenic atom bound at Cys57

PDB DOI: https://doi.org/10.2210/pdb8JBP/pdb

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

Deposited: 2023-05-09 Released: 2024-05-15
Deposition Author(s): Kuaprasert, B., Leartsakulpanich, U., Riangrungroj, P., Pornthanakasem, W., Suginta, W., Robinson, R.C., Zhou, Y., Mungthin, M., Leelayoova, S., Saehlee, S., Choowongkomon, K.
Funding Organization(s): Synchrotron Light Research Institute (SLRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.190 (Depositor), 0.191 (DCC)
R-Value Work:
0.162 (Depositor), 0.162 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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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, C.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: 4,234
Modeled Residue Count: 490
Deposited Residue Count: 542
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	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: 1.45 Å
R-Value Free: 0.190 (Depositor), 0.191 (DCC)
R-Value Work: 0.162 (Depositor), 0.162 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.7	α = 90
b = 79.353	β = 101.24
c = 83.114	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
DENZO	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-05-15

Deposition Author(s):

Leartsakulpanich, U.

Riangrungroj, P.

Pornthanakasem, W.

Choowongkomon, K.

Funding Organization	Location	Grant Number
Synchrotron Light Research Institute (SLRI)	Thailand	SLRI 3-62 and Kasetsart University Research and Development Institute, Kasetsart University, Thailand, Grant Number FF(KU) 6.64

Revision History (Full details and data files)

Version 1.0: 2024-05-15
Type: Initial release

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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.