2CNQ | pdb_00002cnq

Atomic resolution structure of SAICAR-synthase from Saccharomyces cerevisiae complexed with ADP, AICAR, succinate

• PDB DOI: https://doi.org/10.2210/pdb2CNQ/pdb

• Classification: LIGASE
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2006-05-23 Released: 2006-06-08 
• Deposition Author(s): Urusova, D.V., Antonyuk, S.V., Grebenko, A.I., Levdikov, V.M., Barynin, V.V., Popov, A.N., Lamzin, V.S., Melik-Adamyan, W.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 
  0.130 (Depositor), 0.142 (DCC) 
• R-Value Work: 
  0.115 (Depositor), 0.127 (DCC) 
• R-Value Observed: 
  0.116 (Depositor) 

Starting Model: experimental

Literature

Saicar Synthase: Substrate Recognition, Conformational Flexibility and Catalysis.

Urusova, D.V., Antonyuk, S.V., Grebenko, A.I., Levdikov, V.M., Barynin, V.V., Popov, A.N., Lamzin, V.S., Melik-Adamyan, W.R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 37.07 kDa 
• Atom Count: 3,626 
• Modeled Residue Count: 302 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE	A	306	Saccharomyces cerevisiae	Mutation(s): 0  EC: 6.3.2.6
UniProt
Find proteins for P27616 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P27616  Go to UniProtKB:  P27616

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	B [auth A], F [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
AMP	E [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
AMZ	C [auth A], D [auth A]	AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE C9 H15 N4 O8 P NOTGFIUVDGNKRI-UUOKFMHZSA-N
SIN	G [auth A], H [auth A]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
SO4	J [auth A], K [auth A], L [auth A], M [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free:  0.130 (Depositor), 0.142 (DCC) 
• R-Value Work:  0.115 (Depositor), 0.127 (DCC) 
• R-Value Observed: 0.116 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.683	α = 90
b = 61.851	β = 90
c = 76.893	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-08 
Deposition Author(s): Urusova, D.V., Antonyuk, S.V., Grebenko, A.I., Levdikov, V.M., Barynin, V.V., Popov, A.N., Lamzin, V.S., Melik-Adamyan, W.R.

Revision History  

• Version 1.0: 2006-06-08
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2018-12-19
  Changes: Advisory, Atomic model, Data collection, Derived calculations
• Version 2.1: 2019-07-10
  Changes: Data collection, Derived calculations
• Version 2.2: 2019-07-24
  Changes: Data collection
• Version 2.3: 2023-12-13
  Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description
• Version 2.4: 2024-11-13
  Changes: Structure summary