SAXSdb — 3kcz

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

Poly [ADP-ribose] polymerase 2

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	3-aminobenzamide × 1 GLYCEROL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	3-aminobenzamide × 1 GLYCEROL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PARP2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–368； UniProt 235–579 Author chain B； PDBConstruct 24–368； UniProt 235–579

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	3kcz
Deposition date deposition_date	2009-10-22
Structure title title	Human poly(ADP-ribose) polymerase 2, catalytic fragment in complex with an inhibitor 3-aminobenzamide
Keywords keywords	;transferase, enzyme-inhibitor complex, catalytic fragment, Structural Genomics, Structural Genomics Consortium, SGC, Glycosyltransferase, NAD, Nucleus, DNA-binding ;; TRANSFERASE
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.

3kcz__assembly_1__model_1

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

Download this curve (.dat)

3kcz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3kcz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.17 Å
Rg (electron density)	20.99 Å
Total Rg	21.93 Å
Atom count	2821
Residues	353
Excluded volume	50436 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3kcz__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3kcz__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	Poly [ADP-ribose] polymerase 2
Molecular weight formula_weight	41827.9 kDa
EC 编号 ec_number	2.4.2.30
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	6002

MHHHHHHSSGVDLGTENLYFQSMDLRVQELIKLICNVQAMEEMMMEMKYNTKKAPLGKLTVAQIKAGYQSLKKIEDCIRAGQHGRALMEACNEFYTRIPHDFGLRTPPLIRTQKELSEKIQLLEALGDIEIAIKLVKTELQSPEHPLDQHYRNLHCALRPLDHESYEFKVISQYLQSTHAPTHSDYTMTLLDLFEVEKDGEKEAFREDLHNRMLLWHGSRMSNWVGILSHGLRIAHPEAPITGYMFGKGIYFADMSSKSANYCFASRLKNTGLLLLSEVALGQCNELLEANPKAEGLLQGKHSTKGLGKMAPSSAHFVTLNGSTVPLGPASDTGILNPDGYTLNYNEYIVYNPNQVRMRYLLKVQFNF

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	3-aminobenzamide
Molecular weight formula_weight	136.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	387

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3kcza1
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	d3kcza2
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.166.1.2 — Poly(ADP-ribose) polymerase, C-terminal domain

Domain ID domain_id	d3kcza3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3kczb1
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	d3kczb2
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.166.1.2 — Poly(ADP-ribose) polymerase, C-terminal domain

Domain ID domain_id	d3kczb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	3kczA01
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	3kczA02
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	3kczB01
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	3kczB02
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	58.280 Å
Unit-cell length b length_b	134.720 Å
Unit-cell length c length_c	58.250 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	117.67 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	40.970 Å
R factor r_factor	0.1899
R_work r_work	0.1874
R_free r_free	0.2366

Human poly(ADP-ribose) polymerase 2, catalytic fragment in complex with an inhibitor 3-aminobenzamide

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

Poly [ADP-ribose] polymerase 2

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

3kcz__assembly_1__model_1

3kcz__assembly_1__model_1 | I(q)

3kcz__assembly_1__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Human poly(ADP-ribose) polymerase 2, catalytic fragment in complex with an inhibitor 3-aminobenzamide

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

Poly [ADP-ribose] polymerase 2

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

3kcz__assembly_1__model_1

3kcz__assembly_1__model_1 | I(q)

3kcz__assembly_1__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)