5EQC

Structure of the ornithine aminotransferase from Toxoplasma gondii crystallized in presence of oxidized glutathione reveals partial occupancy of PLP at the protein active site

PDB DOI: https://doi.org/10.2210/pdb5EQC/pdb

Classification: TRANSFERASE
Organism(s): Toxoplasma gondii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-11-12 Released: 2016-02-24
Deposition Author(s): Filippova, E.V., Minasov, G., Flores, K., Le, H.V., Silverman, R.B., McLeod, R.L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.181 (Depositor), 0.190 (DCC)
R-Value Work:
0.145 (Depositor), 0.150 (DCC)
R-Value Observed:
0.146 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure of the ornithine aminotransferase from Toxoplasma gondii crystallized in presence of oxidized glutathione reveals partial occupancy of PLP at the protein active site

Filippova, E.V., Minasov, G., Flores, K., Le, H.V., Silverman, R.B., McLeod, R.L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 99.02 kDa
Atom Count: 7,231
Modelled Residue Count: 848
Deposited Residue Count: 882
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ornithine aminotransferase, mitochondrial	A, B	441	Toxoplasma gondii	Mutation(s): 0 Gene Names: TGME49_269110 EC: 2.6.1.13
UniProt
Find proteins for S8EY38 (Toxoplasma gondii (strain ATCC 50611 / Me49)) Explore S8EY38 Go to UniProtKB: S8EY38
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	S8EY38
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth B] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B]	I [auth A], O [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain O [auth B] Interactions & Density Focus chain I [auth A] Focus chain O [auth B]
BTB Query on BTB Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
BGC Query on BGC Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	D [auth A], J [auth B], K [auth B], L [auth B]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
GLC Query on GLC Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B]	F [auth A], G [auth A], H [auth A], N [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B] mmCIF format, chain P [auth B]	P [auth B]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.181 (Depositor), 0.190 (DCC)
R-Value Work: 0.145 (Depositor), 0.150 (DCC)
R-Value Observed: 0.146 (Depositor)

Diffraction Data: https://doi.org/10.18430/m35eqc

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.406	α = 90
b = 109.406	β = 90
c = 109.883	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
BLU-MAX	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-02-24

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2016-02-24
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.3: 2024-05-01
Changes: Derived calculations