SAXSdb — 6pk6

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

Serine/threonine-protein kinase PRP4 homolog

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 657–1005	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1 OND 4-(5-{[(2-aminophenyl)methyl]carbamoyl}thiophen-2-yl)-1-benzothiophene-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1M CAPSO pH 9.5, 20% PEG 8,000	Resolution 2.10 Å R-free 0.216

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 6PK6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4IAN Crystal Structure of apo Human PRPF4B kinase domain Deposited 2012-12-06	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 657–1007（351 aa） Fragment：kinase domain Chain B 657–1007（351 aa） Fragment：kinase domain	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.2M ammonium sulfate, 20-30% PEG 3350 and 0.1M HEPES pH7.0, vapor diffusion, hanging drop, temperature 291K	Resolution 2.44 Å R-free 0.288
4IFC Crystal Structure of ADP-bound Human PRPF4B kinase domain Deposited 2012-12-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 657–1007（351 aa） Fragment：kinase domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	ADP ADENOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.2M ammonium sulfate, 20-30% PEG 3350 and 0.1M HEPES pH7.0 5 mM ADP final concentration added to cryo-protectant solution for soaking of apo crystals, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.13 Å R-free 0.256
4IFC Crystal Structure of ADP-bound Human PRPF4B kinase domain Deposited 2012-12-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 657–1007（351 aa） Fragment：kinase domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	ADP ADENOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.2M ammonium sulfate, 20-30% PEG 3350 and 0.1M HEPES pH7.0 5 mM ADP final concentration added to cryo-protectant solution for soaking of apo crystals, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.13 Å R-free 0.256
4IIR Crystal Structure of AMPPNP-bound Human PRPF4B kinase domain Deposited 2012-12-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 657–1007（351 aa） Fragment：kinase domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 SO4 SULFATE ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.2M ammonium sulfate, 20-30% PEG 3350 and 0.1M HEPES pH7.0, 5 mM AMPPNP final concentration added to cryo-protectant solution for soaking of apo crystals, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.00 Å R-free 0.265
4IIR Crystal Structure of AMPPNP-bound Human PRPF4B kinase domain Deposited 2012-12-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 657–1007（351 aa） Fragment：kinase domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.2M ammonium sulfate, 20-30% PEG 3350 and 0.1M HEPES pH7.0, 5 mM AMPPNP final concentration added to cryo-protectant solution for soaking of apo crystals, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.00 Å R-free 0.265
4IJP Crystal Structure of Human PRPF4B kinase domain in complex with 4-{5-[(2-Chloro-pyridin-4-ylmethyl)-carbamoyl]-thiophen-2-yl}-benzo[b]thiophene-2-carboxylic acid amine Deposited 2012-12-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 657–1007（351 aa） Fragment：kinase domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	1EH 4-(5-{[(2-chloropyridin-4-yl)methyl]carbamoyl}thiophen-2-yl)-1-benzothiophene-2-carboxamide × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.2M ammonium sulfate, 20-30% PEG 3350 and 0.1M HEPES pH7.0 5 mM compound final concentration added to cryo-protectant solution for soaking of apo crystals, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.25 Å R-free 0.265
4IJP Crystal Structure of Human PRPF4B kinase domain in complex with 4-{5-[(2-Chloro-pyridin-4-ylmethyl)-carbamoyl]-thiophen-2-yl}-benzo[b]thiophene-2-carboxylic acid amine Deposited 2012-12-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 657–1007（351 aa） Fragment：kinase domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	1EH 4-(5-{[(2-chloropyridin-4-yl)methyl]carbamoyl}thiophen-2-yl)-1-benzothiophene-2-carboxamide × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.2M ammonium sulfate, 20-30% PEG 3350 and 0.1M HEPES pH7.0 5 mM compound final concentration added to cryo-protectant solution for soaking of apo crystals, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.25 Å R-free 0.265
6CNH Human PRPF4B in complex with Rebastinib Deposited 2018-03-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 657–1005（349 aa） Fragment：UNP residues 657-1005	Not recorded	919 4-[4-({[3-tert-butyl-1-(quinolin-6-yl)-1H-pyrazol-5-yl]carbamoyl}amino)-3-fluorophenoxy]-N-methylpyridine-2-carboxamide × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；18% PEG Smear High, 0.1 M N-(2-acetamido)iminodiacetic acid, 0.2 M ammonium sulfate	Resolution 2.00 Å R-free 0.206
6PJJ Human PRPF4B bound to benzothiophene inhibitor 224 Deposited 2019-06-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 657–1005（349 aa） Chain B 657–1005（349 aa） Chain C 657–1005（349 aa） Chain D 657–1005（349 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	OCJ 4-(5-{[(3-aminophenyl)methyl]carbamoyl}thiophen-2-yl)-1-benzothiophene-2-carboxamide × 4 EDO 1,2-ETHANEDIOL × 8 PO4 PHOSPHATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M HEPES pH 7.5, 0.1M Na/K phosphate, 15% PEG smear high, 10% etylene glycol	Resolution 2.40 Å R-free 0.240
6QX9 Structure of a human fully-assembled precatalytic spliceosome (pre-B complex). Deposited 2019-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 65 PDB declaration: 71-meric	Chain K 1–1007（1007 aa）	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.28 Å
8H6E Cryo-EM structure of human exon-defined spliceosome in the late pre-B state. Deposited 2022-10-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 61-meric	Chain 4Y 1–1007（1007 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8H6J Cryo-EM structure of human exon-defined spliceosome in the mature pre-B state. Deposited 2022-10-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 61-meric	Chain 4Y 1–1007（1007 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.25 Å
8QXD Cryo-EM structure of the cross-exon pre-B complex Deposited 2023-10-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 61-meric	Chain K 1–1007（1007 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.60 Å
8R08 Cryo-EM structure of the cross-exon pre-B+AMPPNP complex Deposited 2023-10-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 64 PDB declaration: 71-meric	Chain K 1–1007（1007 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.10 Å
8R0A Cryo-EM structure of the cross-exon pre-B+5'ss complex Deposited 2023-10-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 62-meric	Chain K 1–1007（1007 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.80 Å
8Y6O Cryo-EM Structure of the human minor pre-B complex (pre-precatalytic spliceosome) U11 and tri-snRNP part Deposited 2024-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 46-meric	Chain Q 1–1007（1007 aa）	Not recorded	MG MAGNESIUM ION × 2 IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.38 Å

13 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PRP4B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–351； UniProt 657–1005

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	6pk6
Deposition date deposition_date	2019-06-28
Structure title title	Human PRPF4B bound to benzothiophene inhibitor 329
Keywords keywords	;Serine/threonine-protein kinase PRP4 homolog, Structural Genomics Consortium, SGC, TRANSFERASE, splicing KINASE PRPF4B, 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	22.64 Å
Radius of gyration Rg (electron density) rg_electron	21.48 Å
Forward intensity I(0) i0	24995000.00
Molecular weight molecular_weight	38938.0 kDa
Excluded volume excluded_volume	49046 Å³
Envelope volume envelope_volume	57485 Å³
Hydration-shell volume shell_volume	22545 Å³
Envelope diameter envelope_diameter	74.6 Å
Shell Rg shell_rg	28.24 Å
Envelope Rg envelope_rg	21.81 Å
Shape Rg shape_rg	21.49 Å
Total Rg total_rg	22.32 Å
Total atoms total_atoms	2737
Residues n_residues	337
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	74.1 Å
Rg (real space) rg_real	22.60 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	2.4990e+07
I(0) uncertainty (real space) i0_real_error	3.2930e+05
Rg (reciprocal space) rg_reciprocal	22.61 Å
I(0) (reciprocal space) i0_reciprocal	25000000.0000
Solution quality estimate total_estimate	0.8965
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.8 Å
Skewness Skewness skewness	0.283
Kurtosis Kurtosis kurtosis	-0.419
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5327000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.989

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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	Serine/threonine-protein kinase PRP4 homolog
Molecular weight formula_weight	40949.3 kDa
EC 编号 ec_number	2.7.11.1
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	2881

SMDFKENPNLRDNWTDAEGYYRVNIGEVLDKRYNVYGYTGQGVFSNVVRARDNARANQEVAVKIIRNNELMQKTGLKELEFLKKLNDADPDDKFHCLRLFRHFYHKQHLCLVFEPLSMNLREVLKKYGKDVGLHIKAVRSYSQQLFLALKLLKRCNILHADIKPDNILVNESKTILKLCDFGSASHVADNDITPYLVSRFYRAPEIIIGKSYDYGIDMWSVGCTLYELYTGKILFPGKTNNHMLKLAMDLKGKMPNKMIRKGVFKDQHFDQNLNFMYIEVDKVTEREKVTVMSTINPTKDLLADLIGCQRLPEDQRKKVHQLKDLLDQILMLDPAKRISINQALQHAFIQE

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	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	4-(5-{[(2-aminophenyl)methyl]carbamoyl}thiophen-2-yl)-1-benzothiophene-2-carboxamide
Molecular weight formula_weight	407.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	141

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6pk6a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	6pk6A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	6pk6A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

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8. Citations (1)

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Unit-cell length a length_a	69.132 Å
Unit-cell length b length_b	69.132 Å
Unit-cell length c length_c	104.533 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	4

Space group space_group	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	69.130 Å
R factor r_factor	0.1904
R_work r_work	0.1890
R_free r_free	0.2165

fit	/app/data/saxs_computation/pk/6pk6/6pk6.fit
pddf	/app/data/pr_computation/pk/6pk6/6pk6.pr.out
profile	/app/data/saxs_computation/pk/6pk6/6pk6.dat

Human PRPF4B bound to benzothiophene inhibitor 329

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

Serine/threonine-protein kinase PRP4 homolog

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