1OBD

SAICAR-synthase complexed with ATP

• PDB DOI: https://doi.org/10.2210/pdb1OBD/pdb

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


• Deposited: 2003-01-30 Released: 2003-03-06 
• Deposition Author(s): Antonyuk, S.V., Grebenko, A.I., Levdikov, V.M., Urusova, D.V., Melik-Adamyan, W.R., Lamzin, V.S., Wilson, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.195 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

X-Ray Structure of Saicar-Synthase Complexed with ATP

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

(2001) Кристаллография 46: 620

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: 35.64 kDa 
• Atom Count: 3,077 
• Modelled Residue Count: 299 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHORIBOSYLAMIDOIMIDAZOLE- 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	B [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
AMP	G [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.195 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.48	α = 90
b = 63.05	β = 90
c = 79.82	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-03-06 
Deposition Author(s): Antonyuk, S.V., Grebenko, A.I., Levdikov, V.M., Urusova, D.V., Melik-Adamyan, W.R., Lamzin, V.S., Wilson, K.

Revision History  

• Version 1.0: 2003-03-06
  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: 2019-05-08
  Changes: Advisory, Data collection, Derived calculations, Experimental preparation, Other
• Version 1.4: 2019-07-24
  Changes: Data collection
• Version 1.5: 2023-12-13
  Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.6: 2024-11-20
  Changes: Structure summary