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1dgm

CRYSTAL STRUCTURE OF ADENOSINE KINASE FROM TOXOPLASMA GONDII

Method: X-RAY DIFFRACTION Dmax: 66.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ADENOSINE KINASE

Toxoplasma gondii

UniProt Q9TVW2

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 1–363 Mutation：L179F MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 ADN ADENOSINE × 1 ACY ACETIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；sodium sulfate, tris HCL, adenosine, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 1.80 Å R-free 0.233

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 1DGM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1LII STRUCTURE OF T. GONDII ADENOSINE KINASE BOUND TO ADENOSINE 2 AND AMP-PCP Deposited 2002-04-17 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 1–363（363 aa）
Not recorded MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 ADN ADENOSINE × 1 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；ammonium sulphate, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.73 Å R-free 0.225
1LIJ STRUCTURE OF T. GONDII ADENOSINE KINASE BOUND TO PRODRUG 2 7-IODOTUBERCIDIN AND AMP-PCP Deposited 2002-04-17 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 1–363（363 aa）
Not recorded CL CHLORIDE ION × 1 MG MAGNESIUM ION × 1 RPP 2-RIBOFURANOSYL-3-IODO-2,3-DIHYDRO-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-YLAMINE × 1 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.50
Resolution 1.86 Å R-free 0.239
1LIK STRUCTURE OF T. GONDII ADENOSINE KINASE BOUND TO ADENOSINE Deposited 2002-04-17 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 1–363（363 aa）
Not recorded SO4 SULFATE ION × 1 CL CHLORIDE ION × 1 ADN ADENOSINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.50
Resolution 2.55 Å R-free 0.200
1LIO STRUCTURE OF APO T. GONDII ADENOSINE KINASE Deposited 2002-04-17 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 1–363（363 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.50
Resolution 2.50 Å R-free 0.260
2A9Y Crystal structure of T. gondii adenosine kinase complexed with N6-dimethyladenosine Deposited 2005-07-12 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 1–363（363 aa）
Mutation：G270S, S360F, L361T, P362S, C363G CL CHLORIDE ION × 1 NA SODIUM ION × 2 ACT ACETATE ION × 1 26A 6N-DIMETHYLADENOSINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；PEG 4000, ammonium acetate, sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.35 Å R-free 0.195
2A9Z Crystal structure of T. gondii adenosine kinase complexed with N6-dimethyladenosine and AMP-PCP Deposited 2005-07-12 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 1–363（363 aa）
Mutation：G270S, S360F, L361T, P362S, C363G CL CHLORIDE ION × 1 NA SODIUM ION × 2 26A 6N-DIMETHYLADENOSINE × 2 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；PEG 4000, ammonium acetate, sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.35 Å R-free 0.196
2AA0 Crystal structure of T. gondii adenosine kinase complexed with 6-methylmercaptopurine riboside Deposited 2005-07-13 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 1–363（363 aa）
Mutation：G270S, S360F, L361T, P362S, C363G CL CHLORIDE ION × 1 NA SODIUM ION × 2 ACT ACETATE ION × 1 MTP 2-HYDROXYMETHYL-5-(6-METHYLSULFANYL-PURIN-9-YL)-TETRAHYDRO-FURAN-3,4-DIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；PEG 4000, ammonium acetate, sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.75 Å R-free 0.240
2AB8 Crystal structure of T. gondii adenosine kinase complexed with 6-methylmercaptopurine riboside and AMP-PCP Deposited 2005-07-14 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 1–363（363 aa）
Mutation：G270S, S360F, L361T, P362S, C363G CL CHLORIDE ION × 1 NA SODIUM ION × 2 MTP 2-HYDROXYMETHYL-5-(6-METHYLSULFANYL-PURIN-9-YL)-TETRAHYDRO-FURAN-3,4-DIOL × 1 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；PEG 4000, ammonium acetate, sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.75 Å R-free 0.230
2ABS Crystal structure of T. gondii adenosine kinase complexed with AMP-PCP Deposited 2005-07-16 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 1–363（363 aa）
Mutation：G270S, S360F, L361T, P362S, C363G CL CHLORIDE ION × 1 NA SODIUM ION × 1 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；295 K；PEG 4000, ammonium acetate, magnesium chloride, sodium citrate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.10 Å R-free 0.167

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ADK_TOXGO
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–363； UniProt 1–363

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 1dgm

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1dgm
Deposition date deposition_date1999-11-24
Structure title titleCRYSTAL STRUCTURE OF ADENOSINE KINASE FROM TOXOPLASMA GONDII
Keywords keywordsTOXOPLASMA GONDII, ADENOSINE KINASE, PURINE METABOLISM, TRANSFERASE; TRANSFERASE
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_guinier20.80 Å
Radius of gyration Rg (electron density) rg_electron19.69 Å
Forward intensity I(0) i023509900.00
Molecular weight molecular_weight37136.0 kDa
Excluded volume excluded_volume46527 ų
Envelope volume envelope_volume53863 ų
Hydration-shell volume shell_volume22398 ų
Envelope diameter envelope_diameter67.5 Å
Shell Rg shell_rg26.56 Å
Envelope Rg envelope_rg19.94 Å
Shape Rg shape_rg19.70 Å
Total Rg total_rg20.56 Å
Total atoms total_atoms2605
Residues n_residues346
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 dmax66.5 Å
Rg (real space) rg_real20.68 Å
Rg uncertainty (real space) rg_real_error0.38 Å
I(0) (real space) i0_real2.3510e+07
I(0) uncertainty (real space) i0_real_error3.3800e+05
Rg (reciprocal space) rg_reciprocal20.71 Å
I(0) (reciprocal space) i0_reciprocal23510000.0000
Solution quality estimate total_estimate0.8923
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.0 Å
Skewness Skewness skewness0.190
Kurtosis Kurtosis kurtosis-0.375
Angular range angular_range— – 0.3800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5624000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.979
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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_idd1dgma_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.72 — Ribokinase-like
Superfamily Superfamily superfamilyc.72.1 — Ribokinase-like
Family Family familyc.72.1.1 — Ribokinase-like

CATH v4.4 (2 domains)

Domain ID domain_id1dgmA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily20 — Ribokinase
Domain ID domain_id1dgmA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1110 — Adenosine kinase, small domain
Homologous superfamily homologous superfamily10 —
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8. Citations (1)

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9. Files and Curves (10)