SAXSdb — 1d6j

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

;ADENOSINE-5'PHOSPHOSULFATE 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	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

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 1D6J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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
1M7H Crystal Structure of APS kinase from Penicillium Chrysogenum: Structure with APS soaked out of one dimer 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 × 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
1M7H Crystal Structure of APS kinase from Penicillium Chrysogenum: Structure with APS soaked out of one dimer 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 × 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
1M7H Crystal Structure of APS kinase from Penicillium Chrysogenum: Structure with APS soaked out of one dimer Deposited 2002-07-19	Different construct Different mutation/modification Different oligomeric state 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 × 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
1M7H Crystal Structure of APS kinase from Penicillium Chrysogenum: Structure with APS soaked out of one dimer Deposited 2002-07-19	Different construct Different mutation/modification Different oligomeric state 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 × 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
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 11 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

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	1d6j
Deposition date deposition_date	1999-10-13
Structure title title	CRYSTAL STRUCTURE OF ADENOSINE 5'-PHOSPHOSULFATE (APS) KINASE FROM PENICILLIUM CHRYSOGENUM
Keywords keywords	APS KINASE, ADENYLYLSULFATE KINASE, SULFATE, NUCLEOTIDE KINASE, TRANSFERASE; 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	21.31 Å
Radius of gyration Rg (electron density) rg_electron	20.54 Å
Forward intensity I(0) i0	27722100.00
Molecular weight molecular_weight	39696.0 kDa
Excluded volume excluded_volume	49448 Å³
Envelope volume envelope_volume	57211 Å³
Hydration-shell volume shell_volume	23158 Å³
Envelope diameter envelope_diameter	78.0 Å
Shell Rg shell_rg	27.42 Å
Envelope Rg envelope_rg	20.93 Å
Shape Rg shape_rg	20.55 Å
Total Rg total_rg	21.38 Å
Total atoms total_atoms	2808
Residues n_residues	359
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	77.6 Å
Rg (real space) rg_real	21.27 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	2.7720e+07
I(0) uncertainty (real space) i0_real_error	3.9920e+05
Rg (reciprocal space) rg_reciprocal	21.28 Å
I(0) (reciprocal space) i0_reciprocal	27720000.0000
Solution quality estimate total_estimate	0.8259
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.2 Å
Skewness Skewness skewness	0.385
Kurtosis Kurtosis kurtosis	-0.014
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9296000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.594; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.992

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	;ADENOSINE-5'PHOSPHOSULFATE 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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3006

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

Entity 2 Entity 2 non-polymer

Description description	L(+)-TARTARIC ACID
Molecular weight formula_weight	150.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	198

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1d6ja_
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	d1d6jb_
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 (2 domains)

Domain ID domain_id	1d6jA00
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	1d6jB00
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	78.862 Å
Unit-cell length b length_b	83.484 Å
Unit-cell length c length_c	141.951 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	36.490 Å
R factor r_factor	0.2070
R_work r_work	0.2070
R_free r_free	0.2490

fit	/app/data/saxs_computation/d6/1d6j/1d6j.fit
pddf	/app/data/pr_computation/d6/1d6j/1d6j.pr.out
profile	/app/data/saxs_computation/d6/1d6j/1d6j.dat

CRYSTAL STRUCTURE OF ADENOSINE 5'-PHOSPHOSULFATE (APS) KINASE FROM PENICILLIUM CHRYSOGENUM

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

;ADENOSINE-5'PHOSPHOSULFATE 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