SAXSdb — 3nm9

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

High mobility group protein D

Drosophila melanogaster

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 6 DNA 10	;DNA 5'-D(GGPCPGPAPTPAPTPCPGP*C)-3' ; × 10 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HMGD_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–73； UniProt 2–74 Author chain D； PDBConstruct 1–73； UniProt 2–74 Author chain G； PDBConstruct 1–73； UniProt 2–74 Author chain J； PDBConstruct 1–73； UniProt 2–74 Author chain M； PDBConstruct 1–73； UniProt 2–74 Author chain P； PDBConstruct 1–73； UniProt 2–74

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	3nm9
Deposition date deposition_date	2010-06-22
Structure title title	HMGD(M13A)-DNA complex
Keywords keywords	High mobility group, DNA bending, non-sequence-specific, HMG domain, chromosomal protein, DNA, GENE REGULATION-DNA complex; GENE REGULATION/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.

3nm9__assembly_1__model_1

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

Download this curve (.dat)

3nm9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3nm9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.34 Å
Rg (electron density)	35.88 Å
Total Rg	36.25 Å
Atom count	5552
Residues	539
Excluded volume	91763 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3nm9__assembly_1__model_1`	hexadecameric （16）	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	High mobility group protein D
Molecular weight formula_weight	8310.4 kDa
Mutation mutation	M13A
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G,J,M,P
Atom count atom_count	5556

SDKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDRAVKEFEANG

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

Entity 2 Entity 2 polymer

Description description	;DNA 5'-D(GGPCPGPAPTPAPTPCPGP*C)-3' ;
Molecular weight formula_weight	3374.2 kDa
Source method src_method	syn
Copy count entity_count	10

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B,C,E,F,H,I,K,L,N,O

GGCGATATCGC

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3nm9a_
Class class	a — All alpha proteins
Fold Fold fold	a.21 — HMG-box
Superfamily Superfamily superfamily	a.21.1 — HMG-box
Family Family family	a.21.1.1 — HMG-box

Domain ID domain_id	d3nm9d_
Class class	a — All alpha proteins
Fold Fold fold	a.21 — HMG-box
Superfamily Superfamily superfamily	a.21.1 — HMG-box
Family Family family	a.21.1.1 — HMG-box

Domain ID domain_id	d3nm9g_
Class class	a — All alpha proteins
Fold Fold fold	a.21 — HMG-box
Superfamily Superfamily superfamily	a.21.1 — HMG-box
Family Family family	a.21.1.1 — HMG-box

Domain ID domain_id	d3nm9j_
Class class	a — All alpha proteins
Fold Fold fold	a.21 — HMG-box
Superfamily Superfamily superfamily	a.21.1 — HMG-box
Family Family family	a.21.1.1 — HMG-box

Domain ID domain_id	d3nm9m_
Class class	a — All alpha proteins
Fold Fold fold	a.21 — HMG-box
Superfamily Superfamily superfamily	a.21.1 — HMG-box
Family Family family	a.21.1.1 — HMG-box

Domain ID domain_id	d3nm9p_
Class class	a — All alpha proteins
Fold Fold fold	a.21 — HMG-box
Superfamily Superfamily superfamily	a.21.1 — HMG-box
Family Family family	a.21.1.1 — HMG-box

CATH v4.4 (6 domains)

Domain ID domain_id	3nm9A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	30 — DNA Binding (I), subunit A
Homologous superfamily homologous superfamily	10 — High mobility group box domain

Domain ID domain_id	3nm9D00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	30 — DNA Binding (I), subunit A
Homologous superfamily homologous superfamily	10 — High mobility group box domain

Domain ID domain_id	3nm9G00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	30 — DNA Binding (I), subunit A
Homologous superfamily homologous superfamily	10 — High mobility group box domain

Domain ID domain_id	3nm9J00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	30 — DNA Binding (I), subunit A
Homologous superfamily homologous superfamily	10 — High mobility group box domain

Domain ID domain_id	3nm9M00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	30 — DNA Binding (I), subunit A
Homologous superfamily homologous superfamily	10 — High mobility group box domain

Domain ID domain_id	3nm9P00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	30 — DNA Binding (I), subunit A
Homologous superfamily homologous superfamily	10 — High mobility group box domain

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Unit-cell length a length_a	44.750 Å
Unit-cell length b length_b	71.700 Å
Unit-cell length c length_c	89.020 Å
Unit-cell angle α angle_alpha	92.49 °
Unit-cell angle β angle_beta	91.12 °
Unit-cell angle γ angle_gamma	107.10 °
Molecules per unit cell Z z_pdb	10

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

Resolution resolution	2.850 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2476
R_work r_work	0.2450
R_free r_free	0.2956

HMGD(M13A)-DNA complex

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

High mobility group protein D

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

3nm9__assembly_1__model_1

3nm9__assembly_1__model_1 | I(q)

3nm9__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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

HMGD(M13A)-DNA complex

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

High mobility group protein D

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

3nm9__assembly_1__model_1

3nm9__assembly_1__model_1 | I(q)

3nm9__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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)