3MEB

Structure of cytoplasmic aspartate aminotransferase from giardia lamblia

PDB DOI: https://doi.org/10.2210/pdb3MEB/pdb

Classification: TRANSFERASE
Organism(s): Giardia lamblia ATCC 50803
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-03-31 Released: 2010-04-21
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.214
R-Value Work: 0.174
R-Value Observed: 0.176

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Structures of aspartate aminotransferases from Trypanosoma brucei, Leishmania major and Giardia lamblia.

Abendroth, J., Choi, R., Wall, A., Clifton, M.C., Lukacs, C.M., Staker, B.L., Van Voorhis, W., Myler, P., Lorimer, D.D., Edwards, T.E.

(2015) Acta Crystallogr Sect F Struct Biol Cryst Commun 71: 566-571

PubMed: 25945710 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S2053230X15001831
Primary Citation of Related Structures:
3MEB, 4EU1, 4H51, 4W5K

PubMed Abstract:
The structures of three aspartate aminotransferases (AATs) from eukaryotic pathogens were solved within the Seattle Structural Genomics Center for Infectious Disease (SSGCID). Both the open and closed conformations of AAT were observed. Pyridoxal phosphate was bound to the active site via a Schiff base to a conserved lysine. An active-site mutant showed that Trypanosoma brucei AAT still binds pyridoxal phosphate even in the absence of the tethering lysine. The structures highlight the challenges for the structure-based design of inhibitors targeting the active site, while showing options for inhibitor design targeting the N-terminal arm.

Organizational Affiliation

Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA.

Macromolecule Content

Total Structure Weight: 101.69 kDa
Atom Count: 7,562
Modelled Residue Count: 852
Deposited Residue Count: 896
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate aminotransferase	A, B	448	Giardia lamblia ATCC 50803	Mutation(s): 0 Gene Names: GL50803_91056 EC: 2.6.1.1
UniProt
Find proteins for A8B1V5 (Giardia intestinalis (strain ATCC 50803 / WB clone C6)) Explore A8B1V5 Go to UniProtKB: A8B1V5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A8B1V5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain O [auth B] MOL2 format, chain D [auth A] MOL2 format, chain O [auth B] mmCIF format, chain D [auth A] mmCIF format, chain O [auth B]	D [auth A], O [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain O [auth B] Interactions & Density Focus chain D [auth A] Focus chain O [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain M [auth B] SDF format, chain P [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth B]	C [auth A], E [auth A], M [auth B], P [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain M [auth B] Focus chain P [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain M [auth B] Focus chain P [auth B]
EDO Query on EDO 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 I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], N [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.214
R-Value Work: 0.174
R-Value Observed: 0.176
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M33MEB

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.58	α = 90
b = 101.15	β = 90.62
c = 81.53	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-04-21

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2010-04-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2015-05-06
Changes: Database references
Version 1.3: 2015-05-13
Changes: Database references
Version 1.4: 2015-05-27
Changes: Database references
Version 1.5: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description