SAXSdb — 1dnk

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

PROTEIN (DEOXYRIBONUCLEASE I (DNASE I) (E.C.3.1.21.1))

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2 其他Polymer 1	;DNA (5'-D(GPGPTPAPTPAPC)-3') ; × 1 ;DNA (5'-D(GPGPTPAPTPAPCP*C)-3') ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 3	Review required

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DRN1_BOVIN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–260； UniProt 23–282

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	1dnk
Deposition date deposition_date	1992-08-10
Structure title title	THE X-RAY STRUCTURE OF THE DNASE I-D(GGTATACC)2 COMPLEX AT 2.3 ANGSTROMS RESOLUTION
Keywords keywords	PROTEIN-DNA COMPLEX, DOUBLE HELIX, HYDROLASE-DNA COMPLEX; HYDROLASE/DNA
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.

1dnk__assembly_1__model_1

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

Download this curve (.dat)

1dnk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1dnk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.61 Å
Rg (electron density)	18.17 Å
Total Rg	19.14 Å
Atom count	2313
Residues	265
Excluded volume	40185 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1dnk__assembly_1__model_1`	trimeric （3）	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	;DNA (5'-D(GPGPTPAPTPAP*C)-3') ;
Molecular weight formula_weight	2137.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B
Atom count atom_count	2390

GGTATAC

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(GPGPTPAPTPAPCPC)-3') ;
Molecular weight formula_weight	2426.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

GGTATACC

Entity 3 Entity 3 polymer

Description description	PROTEIN (DEOXYRIBONUCLEASE I (DNASE I) (E.C.3.1.21.1))
Molecular weight formula_weight	29092.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

LKIAAFNIRTFGETKMSNATLASYIVRIVRRYDIVLIQEVRDSHLVAVGKLLDYLNQDDPNTYHYVVSEPLGRNSYKERYLFLFRPNKVSVLDTYQYDDGCESCGNDSFSREPAVVKFSSHSTKVKEFAIVALHSAPSDAVAEINSLYDVYLDVQQKWHLNDVMLMGDFNADCSYVTSSQWSSIRLRTSSTFQWLIPDSADTTATSTNCAYDRIVVAGSLLQSSVVPGSAAPFDFQAAYGLSNEMALAISDHYPVEVTLT

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	77

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1dnka_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.151 — DNase I-like
Superfamily Superfamily superfamily	d.151.1 — DNase I-like
Family Family family	d.151.1.1 — DNase I-like

CATH v4.4 (1 domains)

Domain ID domain_id	1dnkA00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	10 — Deoxyribonuclease I; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease/exonuclease/phosphatase

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7. Citations (8)

X-ray structure of the DNase I-d(GGTATACC)2 complex at 2.3 A resolution.

J.Mol.Biol. (1992)

PMID: 1518054 · DOI: 10.1016/0022-2836(92)91064-V PRIMARY

DNAse I induced DNA conformation: 2 Angstroms structure of a DNAse-octamer complex

J.Mol.Biol. (1991)

Structure refined to 2 Angstroms of a nicked DNA octanucleotide complex with DNAse I

Nature (1988)

Structure of DNase I at 2.0 Angstroms resolution suggests a mechanism for binding to and cutting DNA

Nature (1986)

Crystallographic refinement and structure of DNAse I at 2 Angstroms resolution

J.Mol.Biol. (1986)

Three-dimensional structure of bovine pancreatic DNAse I at 2.5 Angstroms resolution

Embo J. (1984)

Crystallization and preliminary crystallographic data of bovine pancreatic deoxyribonuclease I

J.Mol.Biol. (1982)

Bovine pancreatic deoxyribonuclease A. Isolation of cyanogen bromide peptides, complete covalent structure of the polypeptide chain

J.Biol.Chem. (1973)

Unit-cell length a length_a	51.100 Å
Unit-cell length b length_b	108.400 Å
Unit-cell length c length_c	62.100 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 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.1880
R_work r_work	—
R_free r_free	—

THE X-RAY STRUCTURE OF THE DNASE I-D(GGTATACC)2 COMPLEX AT 2.3 ANGSTROMS RESOLUTION

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

PROTEIN (DEOXYRIBONUCLEASE I (DNASE I) (E.C.3.1.21.1))

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

1dnk__assembly_1__model_1

1dnk__assembly_1__model_1 | I(q)

1dnk__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 branched

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (8)

THE X-RAY STRUCTURE OF THE DNASE I-D(GGTATACC)2 COMPLEX AT 2.3 ANGSTROMS RESOLUTION

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

PROTEIN (DEOXYRIBONUCLEASE I (DNASE I) (E.C.3.1.21.1))

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

1dnk__assembly_1__model_1

1dnk__assembly_1__model_1 | I(q)

1dnk__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 branched

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (8)