SAXSdb — 9o7r

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform 2 of Adenosine kinase

Homo sapiens

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 × 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

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 9O7R	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BX4 STRUCTURE OF HUMAN ADENOSINE KINASE AT 1.50 ANGSTROMS Deposited 1998-10-13	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 × 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
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

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	P55263-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 121–465； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9o7r
Deposition date deposition_date	2025-04-15
最后修订 last_revision	2026-05-06
Structure title title	Crystal structure of human adenosine kinase (ADK) in complex with inhibitor BKI-1553
Keywords keywords	;SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, adenosine kinase (ADK), inhibitor, TRANSFERASE, TRANSFERASE-TRANSFERASE INHIBITOR complex ;; TRANSFERASE/TRANSFERASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.98 Å
Radius of gyration Rg (electron density) rg_electron	19.79 Å
Forward intensity I(0) i0	29068700.00
Molecular weight molecular_weight	39808.0 kDa
Excluded volume excluded_volume	49085 Å³
Envelope volume envelope_volume	57834 Å³
Hydration-shell volume shell_volume	23639 Å³
Envelope diameter envelope_diameter	69.4 Å
Shell Rg shell_rg	26.99 Å
Envelope Rg envelope_rg	20.11 Å
Shape Rg shape_rg	19.74 Å
Total Rg total_rg	20.82 Å
Total atoms total_atoms	2771
Residues n_residues	340
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	74.6 Å
Rg (real space) rg_real	20.85 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	2.9070e+07
I(0) uncertainty (real space) i0_real_error	3.6460e+05
Rg (reciprocal space) rg_reciprocal	20.87 Å
I(0) (reciprocal space) i0_reciprocal	29070000.0000
Solution quality estimate total_estimate	0.7710
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	27.0 Å
Skewness Skewness skewness	0.173
Kurtosis Kurtosis kurtosis	-0.406
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10280000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.674; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Isoform 2 of Adenosine kinase
Molecular weight formula_weight	52372.4 kDa
EC 编号 ec_number	2.7.1.20
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2781

MAHHHHHHMKSDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGTLEAQTQGPGAAAMTSVRENILFGMGNPLLDISAVVDKDFLDKYSLKPNDQILAEDKHKELFDELVKKFKVEYHAGGSTQNSIKVAQWMIQQPHKAATFFGCIGIDKFGEILKRKAAEAHVDAHYYEQNEQPTGTCAACITGDNRSLIANLAAANCYKKEKHLDLEKNWMLVEKARVCYIAGFFLTVSPESVLKVAHHASENNRIFTLNLSAPFISQFYKESLMKVMPYVDILFGNETEAATFAREQGFETKDIKEIAKKTQALPKMNSKRQRIVIFTQGRDDTIMATESEVTAFAVLDQDQKEIIDTNGAGDAFVGGFLSQLVSDKPLTECIRAGHYAASIIIRRTGCTFPEKPDFH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	1-{4-amino-3-[6-(cyclopropyloxy)naphthalen-2-yl]-1H-pyrazolo[3,4-d]pyrimidin-1-yl}-2-methylpropan-2-ol
Molecular weight formula_weight	389.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	10

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8. Citations (1)

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Unit-cell length a length_a	112.867 Å
Unit-cell length b length_b	112.867 Å
Unit-cell length c length_c	114.473 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.410 Å
Low-resolution limit resolution_low	46.510 Å
R factor r_factor	0.2243
R_work r_work	0.2225
R_free r_free	0.2584

fit	/app/data/saxs_computation/o7/9o7r/9o7r.fit
pddf	/app/data/pr_computation/o7/9o7r/9o7r.pr.out
profile	/app/data/saxs_computation/o7/9o7r/9o7r.dat

Crystal structure of human adenosine kinase (ADK) in complex with inhibitor BKI-1553

1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform 2 of Adenosine kinase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction