SAXSdb — 1nk2

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

HOMEOBOX PROTEIN VND

Drosophila melanogaster

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	;DNA (5'-D(TPGPTPGPTPCPAPAPGPTPGPGPCPTPGPT)-3') ; × 1 ;DNA (5'-D(APCPAPGPCPCPAPCPTPTPGPAPCPAPCPA)-3') ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VND_DROME
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain P； PDBConstruct 1–77； UniProt 61–137

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	1nk2
Deposition date deposition_date	1998-05-06
Structure title title	VND/NK-2 HOMEODOMAIN/DNA COMPLEX, NMR, 20 STRUCTURES
Keywords keywords	HOMEODOMAIN, HOMEOBOX, DNA-BINDING PROTEIN, EMBRYONIC DEVELOPMENT, COMPLEX (HOMEODOMAIN-DNA), DNA BINDING PROTEIN-DNA COMPLEX; DNA BINDING PROTEIN/DNA
Experimental Method method	SOLUTION NMR

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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.

1nk2__assembly_1__model_1

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

Download this curve (.dat)

1nk2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1nk2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.16 Å
Rg (electron density)	17.43 Å
Total Rg	18.23 Å
Atom count	2358
Residues	109
Excluded volume	21193 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1nk2__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	2	`1nk2__assembly_1__model_2`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	3	`1nk2__assembly_1__model_3`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	4	`1nk2__assembly_1__model_4`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	5	`1nk2__assembly_1__model_5`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	6	`1nk2__assembly_1__model_6`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	7	`1nk2__assembly_1__model_7`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	8	`1nk2__assembly_1__model_8`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	9	`1nk2__assembly_1__model_9`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	10	`1nk2__assembly_1__model_10`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	11	`1nk2__assembly_1__model_11`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	12	`1nk2__assembly_1__model_12`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	13	`1nk2__assembly_1__model_13`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	14	`1nk2__assembly_1__model_14`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	15	`1nk2__assembly_1__model_15`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	16	`1nk2__assembly_1__model_16`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	17	`1nk2__assembly_1__model_17`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	18	`1nk2__assembly_1__model_18`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	19	`1nk2__assembly_1__model_19`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	20	`1nk2__assembly_1__model_20`	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 (3)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(TPGPTPGPTPCPAPAPGPTPGPGPCPTPGPT)-3') ;
Molecular weight formula_weight	4960.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	A
Atom count atom_count	47160

TGTGTCAAGTGGCTGT

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(APCPAPGPCPCPAPCPTPTPGPAPCPAPCPA)-3') ;
Molecular weight formula_weight	4836.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

ACAGCCACTTGACACA

Entity 3 Entity 3 polymer

Description description	HOMEOBOX PROTEIN VND
Molecular weight formula_weight	9374.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

ASDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEKGYEGHP

Source Source

Source organism organism	Drosophila melanogaster
Common name common_name	fruit fly
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1nk2p_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.1 — Homeodomain-like
Family Family family	a.4.1.1 — Homeodomain

CATH v4.4 (1 domains)

Domain ID domain_id	1nk2P00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

VND/NK-2 HOMEODOMAIN/DNA COMPLEX, NMR, 20 STRUCTURES

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

HOMEOBOX PROTEIN VND

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

1nk2__assembly_1__model_1

1nk2__assembly_1__model_1 | I(q)

1nk2__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (4)

VND/NK-2 HOMEODOMAIN/DNA COMPLEX, NMR, 20 STRUCTURES

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

HOMEOBOX PROTEIN VND

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

1nk2__assembly_1__model_1

1nk2__assembly_1__model_1 | I(q)

1nk2__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (4)