2CNV | pdb_00002cnv

SAICAR-synthase from Saccharomyces cerevisiae complexed SAICAR

• PDB DOI: https://doi.org/10.2210/pdb2CNV/pdb

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


• Deposited: 2006-05-24 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, V.R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

X-Ray Diffraction Study of the Complex of the Enzyme Saicar Synthase with the Reaction Product

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

(2006) Crystallogr Rep 51: 824

• DOI: https://doi.org/10.1134/S1063774506050129

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: 35.46 kDa 
• Atom Count: 2,914 
• Modeled Residue Count: 300 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SSS	D [auth A]	N-{[5-AMINO-1-(5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1H-IMIDAZOL-4-YL]CARBONYL}-L-ASPARTIC ACID C13 H19 N4 O12 P NAQGHJTUZRHGAC-PSYSQGJASA-N
ASP	B [auth A], C [auth A]	ASPARTIC ACID C4 H7 N O4 CKLJMWTZIZZHCS-REOHCLBHSA-N
SO4	E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.85	α = 90
b = 62.75	β = 90
c = 77.7	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, V.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 1.3: 2019-07-24
  Changes: Data collection, Derived calculations
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary