SAXSdb — 4rdu

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

Homeobox protein DLX-5

Homo sapiens

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	(DC)(DG)(DA)(DC)(DT)(DA)(DA)(DT)(DT)(DA)(DG)(DT)(DC)(DG) × 2 water × 3	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 2	(DC)(DG)(DA)(DC)(DT)(DA)(DA)(DT)(DT)(DA)(DG)(DT)(DC)(DG) × 2 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DLX5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–65； UniProt 135–198 Author chain D； PDBConstruct 2–65； UniProt 135–198

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	4rdu
Deposition date deposition_date	2014-09-19
Structure title title	Crystal structure of a distal-less homeobox protein 5 (Dlx5) from Homo sapiens at 1.85 A resolution
Keywords keywords	;PF00046 family, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, TRANSCRIPTION, TRANSCRIPTION-DNA complex, Partnership for Stem Cell Biology, STEMCELL ;; TRANSCRIPTION/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.

4rdu__assembly_1__model_1

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

Download this curve (.dat)

4rdu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4rdu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.90 Å
Rg (electron density)	14.93 Å
Total Rg	15.86 Å
Atom count	1071
Residues	89
Excluded volume	17464 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4rdu__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4rdu__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	Homeobox protein DLX-5
Molecular weight formula_weight	7663.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	2393

GHMVRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKIMKN

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	(DC)(DG)(DA)(DC)(DT)(DA)(DA)(DT)(DT)(DA)(DG)(DT)(DC)(DG)
Molecular weight formula_weight	4279.8 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B,C,E,F

CGACTAATTAGTCG

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	233

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4rdua_
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.4.1.0 — automated matches

Domain ID domain_id	d4rdud_
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.4.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	4rduA01
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

Domain ID domain_id	4rduD01
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	34.182 Å
Unit-cell length b length_b	42.913 Å
Unit-cell length c length_c	56.104 Å
Unit-cell angle α angle_alpha	84.13 °
Unit-cell angle β angle_beta	77.33 °
Unit-cell angle γ angle_gamma	67.13 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	22.303 Å
R factor r_factor	0.1850
R_work r_work	0.1829
R_free r_free	0.2252

Crystal structure of a distal-less homeobox protein 5 (Dlx5) from Homo sapiens at 1.85 A resolution

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

Homeobox protein DLX-5

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

4rdu__assembly_1__model_1

4rdu__assembly_1__model_1 | I(q)

4rdu__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of a distal-less homeobox protein 5 (Dlx5) from Homo sapiens at 1.85 A resolution

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

Homeobox protein DLX-5

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

4rdu__assembly_1__model_1

4rdu__assembly_1__model_1 | I(q)

4rdu__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)