5E5I

Structure of the ornithine aminotransferase from Toxoplasma gondii in complex with inactivator

PDB DOI: https://doi.org/10.2210/pdb5E5I/pdb

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

Deposited: 2015-10-08 Released: 2016-10-19
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: 1.70 Å
R-Value Free: 0.208
R-Value Work: 0.168
R-Value Observed: 0.171

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of the ornithine aminotransferase from Toxoplasma gondii in complex with inactivator.

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: 98.36 kDa
Atom Count: 7,227
Modelled Residue Count: 842
Deposited Residue Count: 882
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5NJ Query on 5NJ 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]	6-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]-4-oxidanylidene-hexanoic acid C₁₃ H₁₈ N O₈ P QNTFLQLZXLXUGE-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
5JV Query on 5JV Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	4-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]pent-4-enoic acid C₁₃ H₁₇ N₂ O₇ P HRCALJQKZAULQS-MKMNVTDBSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B]	H [auth A], M [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Interactions & Density Focus chain H [auth A] Focus chain M [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [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 E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [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 E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] J [auth B] D [auth A], E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [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 E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.208
R-Value Work: 0.168
R-Value Observed: 0.171
Space Group: P 1
Diffraction Data: https://doi.org/10.18430/m35e5i

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.408	α = 100.87
b = 61.445	β = 92.48
c = 63.665	γ = 108.12

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-10-19

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2016-10-19
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

5E5I

Structure of the ornithine aminotransferase from Toxoplasma gondii in complex with inactivator

Structure of the ornithine aminotransferase from Toxoplasma gondii in complex with inactivator.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)