SAXSdb — 3f21

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

Double-stranded RNA-specific adenosine deaminase

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 2	;DNA (5'-D(DTPDCPDAPDCPDGPDTP*DG)-3') ; × 2 water × 4	Consistent with all polymers
2	Protein–DNA	Homooligomer	Protein 2 DNA 2	;DNA (5'-D(DTPDCPDAPDCPDGPDTP*DG)-3') ; × 2 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DSRAD_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–81； UniProt 133–209 Author chain B； PDBConstruct 5–81； UniProt 133–209 Author chain C； PDBConstruct 5–81； UniProt 133–209

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	3f21
Deposition date deposition_date	2008-10-28
Structure title title	Crystal structure of Zalpha in complex with d(CACGTG)
Keywords keywords	;Protein-Z-DNA complex, Alternative promoter usage, Alternative splicing, Cytoplasm, Disease mutation, DNA-binding, Hydrolase, Metal-binding, mRNA processing, Nucleus, Phosphoprotein, Polymorphism, RNA-binding, RNA-mediated gene silencing, Ubl conjugation, Zinc ;; HYDROLASE
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.

3f21__assembly_1__model_1

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

Download this curve (.dat)

3f21__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3f21__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.70 Å
Rg (electron density)	19.19 Å
Total Rg	19.84 Å
Atom count	1266
Residues	142
Excluded volume	22080 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3f21__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3f21__assembly_2__model_1`	tetrameric （4）	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 (3)

Entity 1 Entity 1 polymer

Description description	Double-stranded RNA-specific adenosine deaminase
Molecular weight formula_weight	9002.3 kDa
EC 编号 ec_number	3.5.4.-
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2099

GSHMLSIYQDQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEAGTPPLWKIAVSTQAWNQHSG

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 polymer

Description description	;DNA (5'-D(DTPDCPDAPDCPDGPDTP*DG)-3') ;
Molecular weight formula_weight	2113.4 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,E,F

TCACGTG

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	203

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3f21a_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.19 — Z-DNA binding domain

Domain ID domain_id	d3f21b_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.19 — Z-DNA binding domain

Domain ID domain_id	d3f21c_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.19 — Z-DNA binding domain

CATH v4.4 (3 domains)

Domain ID domain_id	3f21A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	3f21B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	3f21C00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

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Unit-cell length a length_a	87.365 Å
Unit-cell length b length_b	87.365 Å
Unit-cell length c length_c	72.973 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	24

Space group space_group	P 4 21 2
Space-group number int_tables_number	90
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	—
R_work r_work	0.2380
R_free r_free	0.2790

Crystal structure of Zalpha in complex with d(CACGTG)

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

Double-stranded RNA-specific adenosine deaminase

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

3f21__assembly_1__model_1

3f21__assembly_1__model_1 | I(q)

3f21__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of Zalpha in complex with d(CACGTG)

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

Double-stranded RNA-specific adenosine deaminase

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

3f21__assembly_1__model_1

3f21__assembly_1__model_1 | I(q)

3f21__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)