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1bx4

STRUCTURE OF HUMAN ADENOSINE KINASE AT 1.50 ANGSTROMS

Method: X-RAY DIFFRACTION Dmax: 63.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (ADENOSINE KINASE)

Homo sapiens

UniProt P55263

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 1–345 Not recorded CL CHLORIDE ION × 2 MG MAGNESIUM ION × 3 ADN ADENOSINE × 2 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；20%PEG 4K, 0.16M MGCL2, 0.1M TRIS, PH 7.5 Resolution 1.50 Å R-free 0.226

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 1BX4 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4O1L Human Adenosine Kinase in complex with inhibitor Deposited 2013-12-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 17–362（346 aa） Fragment：UNP residues 17-362
Chain B 17–362（346 aa） Fragment：UNP residues 17-362
Not recorded MG MAGNESIUM ION × 4 HO4 5-ethynyl-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.263
4O1L Human Adenosine Kinase in complex with inhibitor Deposited 2013-12-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 17–362（346 aa） Fragment：UNP residues 17-362
Not recorded MG MAGNESIUM ION × 2 HO4 5-ethynyl-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.263
4O1L Human Adenosine Kinase in complex with inhibitor Deposited 2013-12-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 17–362（346 aa） Fragment：UNP residues 17-362
Not recorded MG MAGNESIUM ION × 2 HO4 5-ethynyl-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.263
9O7P Crystal structure of human adenosine kinase (ADK) in complex with inhibitor BKI-1817 Deposited 2025-04-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–345（345 aa）
Not recorded CL CHLORIDE ION × 3 SO4 SULFATE ION × 15 A1B96 (6M)-6-{4-amino-1-[(1-methylpiperidin-4-yl)methyl]-1H-pyrazolo[3,4-d]pyrimidin-3-yl}quinolin-2(1H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；291 K；2.4M ammonium sulfate, 0.1M Citrate pH 4.0. HosaA.19365.a.VZ21.PC00201 at 18 mg/mL. Cocrystallization with 2mM inhibitor. plate 14484 A12 drop 2, Puck: PSL1601, Cryo: 2.5M lithium sulfate
Resolution 2.51 Å R-free 0.246
9O7Q Crystal structure of human adenosine kinase (ADK) in complex with inhibitor BKI-1676 Deposited 2025-04-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–345（345 aa）
Not recorded A1B95 1-[(3P)-3-[6-(cyclopropyloxy)naphthalen-2-yl]-4-(methylamino)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]-2-methylpropan-2-ol × 1 SO4 SULFATE ION × 13 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；291 K；2.4M ammonium sulfate, 0.1M Citrate pH 4.0. HosaA.19365.a.VZ21.PC00201 at 18 mg/mL. Cocrystallization with 2mM inhibitor. plate 14484 A12/A8 drop 2, Puck: PSL1512, Cryo: 2.5M lithium sulfate
Resolution 2.81 Å R-free 0.265
9O7R Crystal structure of human adenosine kinase (ADK) in complex with inhibitor BKI-1553 Deposited 2025-04-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–345（345 aa）
Not recorded CL CHLORIDE ION × 5 UW5 1-{4-amino-3-[6-(cyclopropyloxy)naphthalen-2-yl]-1H-pyrazolo[3,4-d]pyrimidin-1-yl}-2-methylpropan-2-ol × 1 SO4 SULFATE ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；291 K；2.4M ammonium sulfate, 0.1M Citrate pH 4.0. HosaA.19365.a.VZ21.PC00201 at 18 mg/mL. Cocrystallization with 2mM inhibitor. plate 14484 A12 drop 2, Puck: PSL1502, Cryo: 2.5M lithium sulfate
Resolution 2.41 Å R-free 0.258

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ADK_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–345； UniProt 1–345

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 1bx4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1bx4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1bx4
Deposition date deposition_date1998-10-13
Structure title titleSTRUCTURE OF HUMAN ADENOSINE KINASE AT 1.50 ANGSTROMS
Keywords keywordsHUMAN ADENOSINE KINASE, 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_guinier20.45 Å
Radius of gyration Rg (electron density) rg_electron19.39 Å
Forward intensity I(0) i025988100.00
Molecular weight molecular_weight38991.0 kDa
Excluded volume excluded_volume48793 ų
Envelope volume envelope_volume56973 ų
Hydration-shell volume shell_volume23611 ų
Envelope diameter envelope_diameter65.4 Å
Shell Rg shell_rg26.70 Å
Envelope Rg envelope_rg19.71 Å
Shape Rg shape_rg19.37 Å
Total Rg total_rg20.41 Å
Total atoms total_atoms2739
Residues n_residues342
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 dmax63.4 Å
Rg (real space) rg_real20.30 Å
Rg uncertainty (real space) rg_real_error0.25 Å
I(0) (real space) i0_real2.5990e+07
I(0) uncertainty (real space) i0_real_error2.7860e+05
Rg (reciprocal space) rg_reciprocal20.33 Å
I(0) (reciprocal space) i0_reciprocal25990000.0000
Solution quality estimate total_estimate0.8959
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.1 Å
Skewness Skewness skewness0.105
Kurtosis Kurtosis kurtosis-0.446
Angular range angular_range— – 0.3900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7864000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.988
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1bx4a_
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_id1bx4A01
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_id1bx4A02
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)