4r6e

Human artd1 (parp1) - catalytic domain in complex with inhibitor niraparib

Method: X-RAY DIFFRACTION

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

Poly [ADP-ribose] polymerase 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	2-{4-[(3S)-piperidin-3-yl]phenyl}-2H-indazole-7-carboxamide × 1 SULFATE ION × 1 GLYCEROL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	2-{4-[(3S)-piperidin-3-yl]phenyl}-2H-indazole-7-carboxamide × 1 SULFATE ION × 1 GLYCEROL × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	2-{4-[(3S)-piperidin-3-yl]phenyl}-2H-indazole-7-carboxamide × 1 SULFATE ION × 1 GLYCEROL × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	2-{4-[(3S)-piperidin-3-yl]phenyl}-2H-indazole-7-carboxamide × 1 SULFATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PARP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–351； UniProt 662–1011 Author chain B； PDBConstruct 2–351； UniProt 662–1011 Author chain C； PDBConstruct 2–351； UniProt 662–1011 Author chain D； PDBConstruct 2–351； UniProt 662–1011

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	4r6e
Deposition date deposition_date	2014-08-25
Structure title title	Human artd1 (parp1) - catalytic domain in complex with inhibitor niraparib
Keywords keywords	ADP-RIBOSYLATION, DNA REPAIR, ADP-RIBOSYL TRANSFERASE, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4r6e__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4r6e__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4r6e__assembly_3__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	22.25 Å
Rg (electron density)	20.98 Å
Total Rg	22.09 Å
Atom count	2787
Residues	350
Excluded volume	49994 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4r6e__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4r6e__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4r6e__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4r6e__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Poly [ADP-ribose] polymerase 1
Molecular weight formula_weight	40199.9 kDa
EC 编号 ec_number	2.4.2.30
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	11285

MKSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKTAHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2-{4-[(3S)-piperidin-3-yl]phenyl}-2H-indazole-7-carboxamide
Molecular weight formula_weight	320.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	154

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d4r6ea1
Class class	a — All alpha proteins
Fold Fold fold	a.41 — Domain of poly(ADP-ribose) polymerase
Superfamily Superfamily superfamily	a.41.1 — Domain of poly(ADP-ribose) polymerase
Family Family family	a.41.1.0 — automated matches

Domain ID domain_id	d4r6ea2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.166 — ADP-ribosylation
Superfamily Superfamily superfamily	d.166.1 — ADP-ribosylation
Family Family family	d.166.1.0 — automated matches

Domain ID domain_id	d4r6eb1
Class class	a — All alpha proteins
Fold Fold fold	a.41 — Domain of poly(ADP-ribose) polymerase
Superfamily Superfamily superfamily	a.41.1 — Domain of poly(ADP-ribose) polymerase
Family Family family	a.41.1.0 — automated matches

Domain ID domain_id	d4r6eb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.166 — ADP-ribosylation
Superfamily Superfamily superfamily	d.166.1 — ADP-ribosylation
Family Family family	d.166.1.0 — automated matches

Domain ID domain_id	d4r6ec1
Class class	a — All alpha proteins
Fold Fold fold	a.41 — Domain of poly(ADP-ribose) polymerase
Superfamily Superfamily superfamily	a.41.1 — Domain of poly(ADP-ribose) polymerase
Family Family family	a.41.1.0 — automated matches

Domain ID domain_id	d4r6ec2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.166 — ADP-ribosylation
Superfamily Superfamily superfamily	d.166.1 — ADP-ribosylation
Family Family family	d.166.1.0 — automated matches

Domain ID domain_id	d4r6ed1
Class class	a — All alpha proteins
Fold Fold fold	a.41 — Domain of poly(ADP-ribose) polymerase
Superfamily Superfamily superfamily	a.41.1 — Domain of poly(ADP-ribose) polymerase
Family Family family	a.41.1.0 — automated matches

Domain ID domain_id	d4r6ed2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.166 — ADP-ribosylation
Superfamily Superfamily superfamily	d.166.1 — ADP-ribosylation
Family Family family	d.166.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	4r6eA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	142 — Poly(ADP-ribose) Polymerase; domain 1
Homologous superfamily homologous superfamily	10 — Poly(ADP-ribose) polymerase, regulatory domain

Domain ID domain_id	4r6eA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	228 — Phosphoenolpyruvate Carboxykinase; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4r6eB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	142 — Poly(ADP-ribose) Polymerase; domain 1
Homologous superfamily homologous superfamily	10 — Poly(ADP-ribose) polymerase, regulatory domain

Domain ID domain_id	4r6eB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	228 — Phosphoenolpyruvate Carboxykinase; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4r6eC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	142 — Poly(ADP-ribose) Polymerase; domain 1
Homologous superfamily homologous superfamily	10 — Poly(ADP-ribose) polymerase, regulatory domain

Domain ID domain_id	4r6eC02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	228 — Phosphoenolpyruvate Carboxykinase; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4r6eD01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	142 — Poly(ADP-ribose) Polymerase; domain 1
Homologous superfamily homologous superfamily	10 — Poly(ADP-ribose) polymerase, regulatory domain

Domain ID domain_id	4r6eD02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	228 — Phosphoenolpyruvate Carboxykinase; domain 3
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	104.400 Å
Unit-cell length b length_b	108.630 Å
Unit-cell length c length_c	142.200 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	2.200 Å
Low-resolution limit resolution_low	86.300 Å
R factor r_factor	0.2030
R_work r_work	0.2022
R_free r_free	0.2179

Human artd1 (parp1) - catalytic domain in complex with inhibitor niraparib

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

Poly [ADP-ribose] polymerase 1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4r6e__assembly_3__model_1

4r6e__assembly_3__model_1 | I(q)

4r6e__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Human artd1 (parp1) - catalytic domain in complex with inhibitor niraparib

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

Poly [ADP-ribose] polymerase 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4r6e__assembly_3__model_1

4r6e__assembly_3__model_1 | I(q)

4r6e__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)