SAXSdb — 9dev

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

Protein mono-ADP-ribosyltransferase PARP4

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 1–100	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；2M ammonium sulfate, 0.15M Citric Acid pH3.5	Resolution 1.75 Å R-free 0.188

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 9DEV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
11JF RNA Vault bound to PARP4 MINT, focused refinement (MVP/PARP4/TEP1 NADP sample) Deposited 2026-02-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 1–1724（1724 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 Tris 8.0, 75 mM NaCl, 1.5 mM MgCl2, 1 mM DTT, 1 mM NADP, 0.025% DDM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.85 Å
8SWY PARP4 ART domain bound to NADH Deposited 2023-05-19	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 242–282（41 aa） Chain A 365–573（209 aa）	Not recorded	NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；21% PEG3350, 0.2M sodium citrate tribasic dihydrate, 1% ethylene glycol, 800uM NADH	Resolution 2.55 Å R-free 0.254
8SWY PARP4 ART domain bound to NADH Deposited 2023-05-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 242–282（41 aa） Chain B 365–573（209 aa）	Not recorded	NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；21% PEG3350, 0.2M sodium citrate tribasic dihydrate, 1% ethylene glycol, 800uM NADH	Resolution 2.55 Å R-free 0.254
8SWY PARP4 ART domain bound to NADH Deposited 2023-05-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 242–282（41 aa） Chain C 365–573（209 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；21% PEG3350, 0.2M sodium citrate tribasic dihydrate, 1% ethylene glycol, 800uM NADH	Resolution 2.55 Å R-free 0.254
8SWZ PARP4 ART domain bound to EB47 Deposited 2023-05-19	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 242–282（41 aa） Chain A 365–573（209 aa）	Not recorded	GOL GLYCEROL × 1 UHB 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG3350, 0.2M sodium citrate tribasic dihydrate, 800uM EB47	Resolution 3.00 Å R-free 0.248
8SWZ PARP4 ART domain bound to EB47 Deposited 2023-05-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 242–282（41 aa） Chain B 365–573（209 aa）	Not recorded	GOL GLYCEROL × 1 UHB 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG3350, 0.2M sodium citrate tribasic dihydrate, 800uM EB47	Resolution 3.00 Å R-free 0.248
8SWZ PARP4 ART domain bound to EB47 Deposited 2023-05-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 242–282（41 aa） Chain C 365–573（209 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG3350, 0.2M sodium citrate tribasic dihydrate, 800uM EB47	Resolution 3.00 Å R-free 0.248
8SX1 PARP4 catalytic domain Deposited 2023-05-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 242–573（332 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350 and 0.1 M Bis-Tris pH 6.5	Resolution 4.20 Å R-free 0.331
8SX1 PARP4 catalytic domain Deposited 2023-05-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 242–573（332 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350 and 0.1 M Bis-Tris pH 6.5	Resolution 4.20 Å R-free 0.331
8SX1 PARP4 catalytic domain Deposited 2023-05-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 242–573（332 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350 and 0.1 M Bis-Tris pH 6.5	Resolution 4.20 Å R-free 0.331
8SX1 PARP4 catalytic domain Deposited 2023-05-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 242–573（332 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350 and 0.1 M Bis-Tris pH 6.5	Resolution 4.20 Å R-free 0.331
8SX1 PARP4 catalytic domain Deposited 2023-05-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 242–573（332 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350 and 0.1 M Bis-Tris pH 6.5	Resolution 4.20 Å R-free 0.331
8SX1 PARP4 catalytic domain Deposited 2023-05-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 242–573（332 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350 and 0.1 M Bis-Tris pH 6.5	Resolution 4.20 Å R-free 0.331
8SX1 PARP4 catalytic domain Deposited 2023-05-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 242–573（332 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350 and 0.1 M Bis-Tris pH 6.5	Resolution 4.20 Å R-free 0.331
8SX1 PARP4 catalytic domain Deposited 2023-05-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 242–573（332 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350 and 0.1 M Bis-Tris pH 6.5	Resolution 4.20 Å R-free 0.331
8SX2 PARP4 catalytic domain bound to EB47 Deposited 2023-05-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 242–573（332 aa）	Not recorded	UHB 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350, 0.1 M Bis-Tris pH 6.5, 0.2 M MgCl2, and 600 uM EB47	Resolution 2.95 Å R-free 0.262
8SX2 PARP4 catalytic domain bound to EB47 Deposited 2023-05-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 242–573（332 aa）	Not recorded	UHB 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350, 0.1 M Bis-Tris pH 6.5, 0.2 M MgCl2, and 600 uM EB47	Resolution 2.95 Å R-free 0.262
9BW6 Human Vault Cage in complex with PARP4 Deposited 2024-05-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 156 PDB declaration: 156-meric	Chain B 1–1724（1724 aa） Chain D 1–1724（1724 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM HEPES, 5 mM MgCl2, 5 mM CaCl2, 0.25 mM DTT cryo-EM vitrification conditions Cryogen ETHANE；Vitrification carried out under standard conditions	Resolution 2.90 Å
9BW6 Human Vault Cage in complex with PARP4 Deposited 2024-05-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–1724（1724 aa） Chain D 1–1724（1724 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM HEPES, 5 mM MgCl2, 5 mM CaCl2, 0.25 mM DTT cryo-EM vitrification conditions Cryogen ETHANE；Vitrification carried out under standard conditions	Resolution 2.90 Å
9BW7 Human Vault Cage in complex with PARP4 and NAD+ Deposited 2024-05-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 156 PDB declaration: 156-meric	Chain B 1–1724（1724 aa） Chain D 1–1724（1724 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 78	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM HEPES, 5 mM MgCl2, 5 mM CaCl2, 0.25 mM DTT cryo-EM vitrification conditions Cryogen ETHANE；Vitrification carried out under standard conditions	Resolution 2.90 Å
9BW7 Human Vault Cage in complex with PARP4 and NAD+ Deposited 2024-05-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–1724（1724 aa） Chain D 1–1724（1724 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM HEPES, 5 mM MgCl2, 5 mM CaCl2, 0.25 mM DTT cryo-EM vitrification conditions Cryogen ETHANE；Vitrification carried out under standard conditions	Resolution 2.90 Å
9DFO PARP4 BRCT domain K31Q mutant Deposited 2024-08-30	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–100（100 aa）	Mutation：K31Q	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；31% PEG3350, 0.2M ammonium sulfate and 0.1M sodium acetate pH 4.6	Resolution 1.90 Å R-free 0.208
9DFP PARP4 BRCT domain K23/24Q mutant Deposited 2024-08-30	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–100（100 aa）	Mutation：K23Q,K24Q	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；27% PEG3350, 0.2M ammonium sulfate and 0.1M sodium acetate pH 4.6	Resolution 1.92 Å R-free 0.219
9DFQ PARP4 BRCT domain F39Q mutant Deposited 2024-08-30	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–100（100 aa）	Mutation：F39Q	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2 M ammonium sulfate and 0.1 M sodium acetate pH 4.6	Resolution 2.10 Å R-free 0.230
9DFR PARP4 BRCT domain F39A mutant Deposited 2024-08-30	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–100（100 aa）	Mutation：F39A	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；27% PEG3350, 0.2M ammonium sulfate and 0.1M sodium acetate pH 4.6	Resolution 1.90 Å R-free 0.218

11 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PARP4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–100； UniProt 1–100

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	9dev
Deposition date deposition_date	2024-08-29
Structure title title	PARP4 BRCT domain
Keywords keywords	PARP family, ADP-ribosyltransferase, marylation, vault, 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	14.37 Å
Radius of gyration Rg (electron density) rg_electron	12.91 Å
Forward intensity I(0) i0	2588320.00
Molecular weight molecular_weight	11417.0 kDa
Excluded volume excluded_volume	14447 Å³
Envelope volume envelope_volume	16140 Å³
Hydration-shell volume shell_volume	10725 Å³
Envelope diameter envelope_diameter	45.1 Å
Shell Rg shell_rg	18.51 Å
Envelope Rg envelope_rg	13.23 Å
Shape Rg shape_rg	12.87 Å
Total Rg total_rg	14.35 Å
Total atoms total_atoms	804
Residues n_residues	97
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	45.9 Å
Rg (real space) rg_real	14.28 Å
Rg uncertainty (real space) rg_real_error	0.21 Å
I(0) (real space) i0_real	2.5880e+06
I(0) uncertainty (real space) i0_real_error	2.7760e+04
Rg (reciprocal space) rg_reciprocal	14.29 Å
I(0) (reciprocal space) i0_reciprocal	2588000.0000
Solution quality estimate total_estimate	0.8836
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.4 Å
Skewness Skewness skewness	0.125
Kurtosis Kurtosis kurtosis	-0.323
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	474000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.832; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.995

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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	Protein mono-ADP-ribosyltransferase PARP4
Molecular weight formula_weight	11711.7 kDa
EC 编号 ec_number	2.4.2.-
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	918

MVMGIFANCIFCLKVKYLPQQQKKKLQTDIKENGGKFSFSLNPQCTHIILDNADVLSQYQLNSIQKNHVHIANPDFIWKSIREKRLLDVKNYDPYKPLDI

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	81

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8. Citations (1)

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Unit-cell length a length_a	114.428 Å
Unit-cell length b length_b	114.428 Å
Unit-cell length c length_c	114.428 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	48

Space group space_group	F 2 3
Space-group number int_tables_number	196
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	19.350 Å
R factor r_factor	0.1753
R_work r_work	0.1746
R_free r_free	0.1876

fit	/app/data/saxs_computation/de/9dev/9dev.fit
pddf	/app/data/pr_computation/de/9dev/9dev.pr.out
profile	/app/data/saxs_computation/de/9dev/9dev.dat

PARP4 BRCT domain

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

Protein mono-ADP-ribosyltransferase PARP4

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