7KDS | pdb_00007kds

Crystal structure of Acetyl-CoA synthetase 2 in complex with Adenosine-5'-propylphosphate from Candida albicans

PDB DOI: https://doi.org/10.2210/pdb7KDS/pdb

Classification: LIGASE
Organism(s): Candida albicans SC5314
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2020-10-09 Released: 2020-11-11
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.267 (Depositor), 0.267 (DCC)
R-Value Work:
0.232 (Depositor), 0.231 (DCC)
R-Value Observed:
0.235 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of Acetyl-CoA synthetase 2 in complex with Adenosine-5'-propylphosphate from Candida albicans

Abendroth, J., Fox III, D., DeBouver, N.D., Krysan, D.J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 76.32 kDa
Atom Count: 4,832
Modeled Residue Count: 654
Deposited Residue Count: 686
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-coenzyme A synthetase 2	A	686	Candida albicans SC5314	Mutation(s): 1 Gene Names: ACS2, CAALFM_C104290CA, CaO19.1064, CaO19.8666 EC: 6.2.1.1
UniProt
Find proteins for Q8NJN3 (Candida albicans (strain SC5314 / ATCC MYA-2876)) Explore Q8NJN3 Go to UniProtKB: Q8NJN3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NJN3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PRX (Subject of Investigation/LOI) Query on PRX Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ADENOSINE-5'-MONOPHOSPHATE-PROPYL ESTER C₁₃ H₂₀ N₅ O₇ P XAMXMSZRQHPMRX-QYVSTXNMSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.267 (Depositor), 0.267 (DCC)
R-Value Work: 0.232 (Depositor), 0.231 (DCC)
R-Value Observed: 0.235 (Depositor)

Diffraction Data:

Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.92	α = 90
b = 166.92	β = 90
c = 166.92	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-11-11

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2020-11-11
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description

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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.