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1obd

SAICAR-synthase complexed with ATP

Method: X-RAY DIFFRACTION Dmax: 69.0 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PHOSPHORIBOSYLAMIDOIMIDAZOLE- SUCCINOCARBOXAMIDE SYNTHASE

OrganismNot specified

UniProt P27616

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 2–306 Non-standard monomer：Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 1 SO4 SULFATE ION × 2 MG MAGNESIUM ION × 2 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；THE HANGING DROPS CONTAINED PROTEIN AT A CONCENTRATION OF 8 - 15 MG/ML, 50 MM TRIS-HCL BUFFER, PH 7.0, 40 MM ASPARTIC ACID AND 1.0 - 1.25 M AMMONIUM SULPHATE. THE WELL CONTAINED THE SAME ABOVE BUFFER PLUS 2.25 M AMMONIUM SULPHATE Resolution 1.40 Å R-free 0.195

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1OBD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A48 SAICAR SYNTHASE Deposited 1998-02-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–306（305 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å
1OBG SAICAR-synthase complexed with ATP Deposited 2003-01-30 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–306（305 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 2 SO4 SULFATE ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；40MM ASP. ASID, 10MM MGCL2, 25MM ATP, 2.26 M (NH4)2(SO4), 5, pH 4.50
Resolution 2.05 Å R-free 0.206
2CNQ Atomic resolution structure of SAICAR-synthase from Saccharomyces cerevisiae complexed with ADP, AICAR, succinate Deposited 2006-05-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–306（305 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ADP ADENOSINE-5'-DIPHOSPHATE × 2 AMZ AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE × 2 AMP ADENOSINE MONOPHOSPHATE × 1 SIN SUCCINIC ACID × 2 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；AMMONIUM SUPHATE, ATP, AICAR, MG, ASP, pH 7.50
Resolution 1.00 Å R-free 0.130
2CNU Atomic resolution structure of SAICAR-synthase from Saccharomyces cerevisiae complexed with aspartic acid Deposited 2006-05-24 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–306（305 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ASP ASPARTIC ACID × 3 SO4 SULFATE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；TRIS-HCL BUFFER, PH 7.5, ASPARTIC ACID, AMMONIUM SULPHATE
Resolution 1.05 Å R-free 0.159
2CNV SAICAR-synthase from Saccharomyces cerevisiae complexed SAICAR Deposited 2006-05-24 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–306（305 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ASP ASPARTIC ACID × 2 SSS N-{[5-AMINO-1-(5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1H-IMIDAZOL-4-YL]CARBONYL}-L-ASPARTIC ACID × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；AMMONIUM SULPHATE, ASPARTIC ACID, TRIS-HCL BUFFER, pH 7.50
Resolution 2.00 Å R-free 0.238

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PUR7_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–306； UniProt 2–306

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1obd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1obd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1obd
Deposition date deposition_date2003-01-30
Structure title titleSAICAR-synthase complexed with ATP
Keywords keywordsSYNTHETASE, ATP BINDING PROTEIN, PHOSPHORIBOSYLAMINOIMIDAZOLESUCCINOCARBOXAMIDE (SAICAR) SYNTHASE, PURINE BIOSYNTHESIS, LIGASE; LIGASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.30 Å
Radius of gyration Rg (electron density) rg_electron19.44 Å
Forward intensity I(0) i020722200.00
Molecular weight molecular_weight34785.0 kDa
Excluded volume excluded_volume43643 ų
Envelope volume envelope_volume50393 ų
Hydration-shell volume shell_volume21412 ų
Envelope diameter envelope_diameter69.8 Å
Shell Rg shell_rg26.15 Å
Envelope Rg envelope_rg19.68 Å
Shape Rg shape_rg19.43 Å
Total Rg total_rg20.38 Å
Total atoms total_atoms2447
Residues n_residues298
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax69.0 Å
Rg (real space) rg_real20.19 Å
Rg uncertainty (real space) rg_real_error0.45 Å
I(0) (real space) i0_real2.0720e+07
I(0) uncertainty (real space) i0_real_error2.3300e+05
Rg (reciprocal space) rg_reciprocal20.21 Å
I(0) (reciprocal space) i0_reciprocal20720000.0000
Solution quality estimate total_estimate0.6314
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary25.6 Å
Skewness Skewness skewness0.197
Kurtosis Kurtosis kurtosis-0.344
Angular range angular_range— – 0.3900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5435000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.751; Stabil: 0.998; Sysdev: 0.319; Positv: 1.000; Valcen: 1.000; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1obda_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.143 — SAICAR synthase-like
Superfamily Superfamily superfamilyd.143.1 — SAICAR synthase-like
Family Family familyd.143.1.1 — SAICAR synthase

CATH v4.4 (2 domains)

Domain ID domain_id1obdA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id1obdA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily20 — ATP-grasp fold, B domain
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8. Citations (2)

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9. Files and Curves (10)