SAXSdb — 1m7h

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

Adenylylsulfate kinase

Penicillium chrysogenum

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 1–211 Chain B； UniProt 1–211	Not recorded	SO4 SULFATE ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ADX ADENOSINE-5'-PHOSPHOSULFATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；Na monobasic phosphate, K dibasic phosphate, succinate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.258
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–211 Chain D； UniProt 1–211	Not recorded	SO4 SULFATE ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ADX ADENOSINE-5'-PHOSPHOSULFATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；Na monobasic phosphate, K dibasic phosphate, succinate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.258
3	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–211 Chain B； UniProt 1–211 Chain C； UniProt 1–211 Chain D； UniProt 1–211	Not recorded	SO4 SULFATE ION × 12 ADP ADENOSINE-5'-DIPHOSPHATE × 4 ADX ADENOSINE-5'-PHOSPHOSULFATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；Na monobasic phosphate, K dibasic phosphate, succinate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.258
4	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–211 Chain B； UniProt 1–211 Chain C； UniProt 1–211 Chain D； UniProt 1–211	Not recorded	SO4 SULFATE ION × 12 ADP ADENOSINE-5'-DIPHOSPHATE × 4 ADX ADENOSINE-5'-PHOSPHOSULFATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；Na monobasic phosphate, K dibasic phosphate, succinate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 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 1M7H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D6J CRYSTAL STRUCTURE OF ADENOSINE 5'-PHOSPHOSULFATE (APS) KINASE FROM PENICILLIUM CHRYSOGENUM Deposited 1999-10-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–211（211 aa） Chain B 1–211（211 aa）	Not recorded	TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH；pH 6；298 K；1.0 M NA/K TARTRATE, O.1 M MES, PH 6.0, 0.5% POLYETHYLINIMINE, BATCH, temperature 298K	Resolution 2.00 Å R-free 0.249
1M7G Crystal structure of APS kinase from Penicillium Chrysogenum: Ternary structure with ADP and APS Deposited 2002-07-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–211（211 aa） Chain B 1–211（211 aa）	Not recorded	SO4 SULFATE ION × 4 AV2 ADENOSINE-5'-DIPHOSPHATE-2',3'-VANADATE × 1 ADX ADENOSINE-5'-PHOSPHOSULFATE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；Na monobasic phosphate, K dibasic phosphate, succinate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.43 Å R-free 0.205
1M7G Crystal structure of APS kinase from Penicillium Chrysogenum: Ternary structure with ADP and APS Deposited 2002-07-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–211（211 aa） Chain D 1–211（211 aa）	Not recorded	SO4 SULFATE ION × 2 AV2 ADENOSINE-5'-DIPHOSPHATE-2',3'-VANADATE × 1 ADX ADENOSINE-5'-PHOSPHOSULFATE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；Na monobasic phosphate, K dibasic phosphate, succinate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.43 Å R-free 0.205
1M7G Crystal structure of APS kinase from Penicillium Chrysogenum: Ternary structure with ADP and APS Deposited 2002-07-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–211（211 aa） Chain B 1–211（211 aa） Chain C 1–211（211 aa） Chain D 1–211（211 aa）	Not recorded	SO4 SULFATE ION × 6 AV2 ADENOSINE-5'-DIPHOSPHATE-2',3'-VANADATE × 2 ADX ADENOSINE-5'-PHOSPHOSULFATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；Na monobasic phosphate, K dibasic phosphate, succinate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.43 Å R-free 0.205
1M7G Crystal structure of APS kinase from Penicillium Chrysogenum: Ternary structure with ADP and APS Deposited 2002-07-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–211（211 aa） Chain B 1–211（211 aa） Chain C 1–211（211 aa） Chain D 1–211（211 aa）	Not recorded	SO4 SULFATE ION × 6 AV2 ADENOSINE-5'-DIPHOSPHATE-2',3'-VANADATE × 2 ADX ADENOSINE-5'-PHOSPHOSULFATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；Na monobasic phosphate, K dibasic phosphate, succinate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.43 Å R-free 0.205
1M7G Crystal structure of APS kinase from Penicillium Chrysogenum: Ternary structure with ADP and APS Deposited 2002-07-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–211（211 aa） Chain B 1–211（211 aa） Chain C 1–211（211 aa） Chain D 1–211（211 aa）	Not recorded	SO4 SULFATE ION × 6 AV2 ADENOSINE-5'-DIPHOSPHATE-2',3'-VANADATE × 2 ADX ADENOSINE-5'-PHOSPHOSULFATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；Na monobasic phosphate, K dibasic phosphate, succinate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.43 Å R-free 0.205
3CR7 Crystal structure of N-terminal truncation of APS Kinase from Penicillium chrysogenum: Ternary structure with ADP and PAPS Deposited 2008-04-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–211（189 aa） Fragment：UNP residues 23-211 Chain B 23–211（189 aa） Fragment：UNP residues 23-211	Not recorded	CL CHLORIDE ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 PPS 3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；bis tris, PEG 3350, ammonium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.279
3CR7 Crystal structure of N-terminal truncation of APS Kinase from Penicillium chrysogenum: Ternary structure with ADP and PAPS Deposited 2008-04-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 23–211（189 aa） Fragment：UNP residues 23-211 Chain D 23–211（189 aa） Fragment：UNP residues 23-211	Not recorded	CL CHLORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 2 PPS 3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；bis tris, PEG 3350, ammonium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.279

3 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KAPS_PENCH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–211； UniProt 1–211 Author chain B； PDBConstruct 1–211； UniProt 1–211 Author chain C； PDBConstruct 1–211； UniProt 1–211 Author chain D； PDBConstruct 1–211； UniProt 1–211

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	1m7h
Deposition date deposition_date	2002-07-19
Structure title title	Crystal Structure of APS kinase from Penicillium Chrysogenum: Structure with APS soaked out of one dimer
Keywords keywords	APS kinase, Adenylylsulfate kinase, Transferase, sulfate metabolism, Nucleotide 2 kinase; TRANSFERASE
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	37.43 Å
Radius of gyration Rg (electron density) rg_electron	37.38 Å
Forward intensity I(0) i0	148873000.00
Molecular weight molecular_weight	94045.0 kDa
Excluded volume excluded_volume	115790 Å³
Envelope volume envelope_volume	153640 Å³
Hydration-shell volume shell_volume	34699 Å³
Envelope diameter envelope_diameter	127.2 Å
Shell Rg shell_rg	42.58 Å
Envelope Rg envelope_rg	36.76 Å
Shape Rg shape_rg	37.37 Å
Total Rg total_rg	37.73 Å
Total atoms total_atoms	6612
Residues n_residues	805
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	127.4 Å
Rg (real space) rg_real	37.69 Å
Rg uncertainty (real space) rg_real_error	1.43 Å
I(0) (real space) i0_real	1.4890e+08
I(0) uncertainty (real space) i0_real_error	2.7560e+06
Rg (reciprocal space) rg_reciprocal	37.54 Å
I(0) (reciprocal space) i0_reciprocal	148800000.0000
Solution quality estimate total_estimate	0.8343
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	27.3 Å
Skewness Skewness skewness	0.366
Kurtosis Kurtosis kurtosis	-0.651
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	38970000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.724; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.756; Smooth: 0.914

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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	Adenylylsulfate kinase
Molecular weight formula_weight	23804.8 kDa
EC 编号 ec_number	2.7.1.25
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7111

MSTNITFHASALTRSERTELRNQRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIRFGLNKDLGFSEADRNENIRRIAEVAKLFADSNSIAITSFISPYRKDRDTARQLHEVATPGEETGLPFVEVYVDVPVEVAEQRDPKGLYKKAREGVIKEFTGISAPYEAPANPEVHVKNYELPVQDAVKQIIDYLDTKGYLPAKKE

来源 Source

来源生物 organism	Penicillium chrysogenum
NCBI Class编号 ncbi_taxonomy_id	5076
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-PHOSPHOSULFATE
Molecular weight formula_weight	427.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	499

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1m7ha_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.4 — Adenosine-5'phosphosulfate kinase (APS kinase)

Domain ID domain_id	d1m7hb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.4 — Adenosine-5'phosphosulfate kinase (APS kinase)

Domain ID domain_id	d1m7hc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.4 — Adenosine-5'phosphosulfate kinase (APS kinase)

Domain ID domain_id	d1m7hd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.4 — Adenosine-5'phosphosulfate kinase (APS kinase)

CATH v4.4 (4 domains)

Domain ID domain_id	1m7hA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1m7hB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1m7hC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1m7hD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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8. Citations (1)

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Unit-cell length a length_a	83.601 Å
Unit-cell length b length_b	83.688 Å
Unit-cell length c length_c	138.677 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	29.910 Å
R factor r_factor	0.2170
R_work r_work	0.2150
R_free r_free	0.2580

fit	/app/data/saxs_computation/m7/1m7h/1m7h.fit
pddf	/app/data/pr_computation/m7/1m7h/1m7h.pr.out
profile	/app/data/saxs_computation/m7/1m7h/1m7h.dat

Crystal Structure of APS kinase from Penicillium Chrysogenum: Structure with APS soaked out of one dimer

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

Adenylylsulfate 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