2QGA

Plasmodium vivax adenylosuccinate lyase Pv003765 with AMP bound

PDB DOI: https://doi.org/10.2210/pdb2QGA/pdb

Classification: LYASE
Organism(s): Plasmodium vivax
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-06-28 Released: 2007-07-24
Deposition Author(s): Lunin, V.V., Wernimont, A.K., Lew, J., Kozieradzki, I., Bochkarev, A., Arrowsmith, C.H., Sundstrom, M., Weigelt, J., Edwards, A.E., Hui, R., Hills, T., Altamentova, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.210
R-Value Work: 0.175
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Plasmodium vivax adenylosuccinate lyase Pv003765 with AMP bound

Lunin, V.V., Wernimont, A.K., Lew, J., Kozieradzki, I., Bochkarev, A., Arrowsmith, C.H., Sundstrom, M., Weigelt, J., Edwards, A.E., Hui, R., Hills, T., Altamentova, S., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 107.65 kDa
Atom Count: 8,242
Modelled Residue Count: 909
Deposited Residue Count: 930
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylosuccinate lyase	A [auth B], B [auth C]	465	Plasmodium vivax	Mutation(s): 0 Gene Names: asl EC: 4.3.2.2
UniProt
Find proteins for A5KBL5 (Plasmodium vivax (strain Salvador I)) Explore A5KBL5 Go to UniProtKB: A5KBL5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5KBL5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain J [auth C] MOL2 format, chain F [auth B] MOL2 format, chain J [auth C]	F [auth B], J [auth C]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain F [auth B] Focus chain J [auth C] Interactions & Density Focus chain F [auth B] Focus chain J [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth B] SDF format, chain H [auth C] SDF format, chain I [auth C] MOL2 format, chain E [auth B] MOL2 format, chain D [auth B] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C]	D [auth B], E [auth B], H [auth C], I [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth B] Focus chain E [auth B] Focus chain H [auth C] Focus chain I [auth C] Interactions & Density Focus chain D [auth B] Focus chain E [auth B] Focus chain H [auth C] Focus chain I [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain G [auth C] MOL2 format, chain C [auth B] MOL2 format, chain G [auth C]	C [auth B], G [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain G [auth C] Interactions & Density Focus chain C [auth B] Focus chain G [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.210
R-Value Work: 0.175
R-Value Observed: 0.177
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.247	α = 90
b = 179.545	β = 99.37
c = 68.575	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
d*TREK	data reduction
d*TREK	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-07-24

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2007-07-24
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

2QGA

Plasmodium vivax adenylosuccinate lyase Pv003765 with AMP bound

Plasmodium vivax adenylosuccinate lyase Pv003765 with AMP bound

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)