SAXSdb — 4o1l

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

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 17–362 Chain B； UniProt 17–362	Fragment：UNP residues 17-362	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 experimental conditions	Resolution 2.50 Å R-free 0.263
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 17–362	Fragment：UNP residues 17-362	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 experimental conditions	Resolution 2.50 Å R-free 0.263
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 17–362	Fragment：UNP residues 17-362	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 experimental conditions	Resolution 2.50 Å R-free 0.263

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 4O1L	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 construct 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
9O7P Crystal structure of human adenosine kinase (ADK) in complex with inhibitor BKI-1817 Deposited 2025-04-15	Different construct 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 construct 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 construct 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 4 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 1–346； UniProt 17–362 Author chain B； PDBConstruct 1–346； UniProt 17–362

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	4o1l
Deposition date deposition_date	2013-12-16
Structure title title	Human Adenosine Kinase in complex with inhibitor
Keywords keywords	Adenosine Kinase, 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	29.50 Å
Radius of gyration Rg (electron density) rg_electron	28.93 Å
Forward intensity I(0) i0	89013300.00
Molecular weight molecular_weight	75044.0 kDa
Excluded volume excluded_volume	94171 Å³
Envelope volume envelope_volume	115030 Å³
Hydration-shell volume shell_volume	33469 Å³
Envelope diameter envelope_diameter	103.6 Å
Shell Rg shell_rg	35.83 Å
Envelope Rg envelope_rg	29.29 Å
Shape Rg shape_rg	28.93 Å
Total Rg total_rg	29.55 Å
Total atoms total_atoms	5281
Residues n_residues	665
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	98.9 Å
Rg (real space) rg_real	29.59 Å
Rg uncertainty (real space) rg_real_error	0.73 Å
I(0) (real space) i0_real	8.9010e+07
I(0) uncertainty (real space) i0_real_error	1.2690e+06
Rg (reciprocal space) rg_reciprocal	29.55 Å
I(0) (reciprocal space) i0_reciprocal	89010000.0000
Solution quality estimate total_estimate	0.8727
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	29.3 Å
Skewness Skewness skewness	0.411
Kurtosis Kurtosis kurtosis	-0.489
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	30450000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.805; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.949; Smooth: 0.975

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Adenosine kinase
Molecular weight formula_weight	38817.3 kDa
EC 编号 ec_number	2.7.1.20
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5322

APQALRENILFGMGNPLLDISAVVDKDFLDKYSLKPNDQILAEDKHKELFDELVKKFKVEYHAGGSTQNSIKVAQWMIQQPHKAATFFGCIGIDKFGEILKRKAAEAHVDAHYYEQNEQPTGTCAACITGDNRSLIANLAAANCYKKEKHLDLEKNWMLVEKARVCYIAGFFLTVSPESVLKVAHHASENNRIFTLNLSAPFISQFYKESLMKVMPYVDILFGNETEAATFAREQGFETKDIKEIAKKTQALPKMNSKRQRIVIFTQGRDDTIMATESEVTAFAVLDQDQKEIIDTNGAGDAFVGGFLSQLVSDKPLTECIRAGHYAASIIIRRTGCTFPEKPDFH

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

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	5-ethynyl-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine
Molecular weight formula_weight	290.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	41

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4o1la_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.72 — Ribokinase-like
Superfamily Superfamily superfamily	c.72.1 — Ribokinase-like
Family Family family	c.72.1.1 — Ribokinase-like

Domain ID domain_id	d4o1lb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.72 — Ribokinase-like
Superfamily Superfamily superfamily	c.72.1 — Ribokinase-like
Family Family family	c.72.1.1 — Ribokinase-like

CATH v4.4 (4 domains)

Domain ID domain_id	4o1lA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily	20 — Ribokinase

Domain ID domain_id	4o1lA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1110 — Adenosine kinase, small domain
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4o1lB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily	20 — Ribokinase

Domain ID domain_id	4o1lB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1110 — Adenosine kinase, small domain
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	67.310 Å
Unit-cell length b length_b	156.590 Å
Unit-cell length c length_c	58.210 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 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	156.590 Å
R factor r_factor	0.1996
R_work r_work	0.1961
R_free r_free	0.2628

fit	/app/data/saxs_computation/o1/4o1l/4o1l.fit
pddf	/app/data/pr_computation/o1/4o1l/4o1l.pr.out
profile	/app/data/saxs_computation/o1/4o1l/4o1l.dat

Human Adenosine Kinase in complex with inhibitor

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

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