SAXSdb — 5mhj

▼

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

Major viral transcription factor ICP4

Human herpesvirus 1 (strain 17)

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(PCPGPAPTPCPGPTPCPC)-3') ; × 1 ;DNA (5'-D(PCPGPAPTPCPGPTPCPC)-3') ; × 1 ACETIC ACID × 2 CHLORIDE ION × 1 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ICP4_HHV11
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–201； UniProt 288–487 Author chain B； PDBConstruct 2–201； UniProt 288–487

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5mhj
Deposition date deposition_date	2016-11-24
Structure title title	ICP4 DNA-binding domain, lacking intrinsically disordered region, in complex with 12mer DNA duplex from its own promoter
Keywords keywords	Transcription factor, Dimer, Herpes, Virus, transcription; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

▼

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.

5mhj__assembly_1__model_1

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

Download this curve (.dat)

5mhj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5mhj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.40 Å
Rg (electron density)	21.34 Å
Total Rg	22.18 Å
Atom count	3230
Residues	399
Excluded volume	55638 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5mhj__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Major viral transcription factor ICP4
Molecular weight formula_weight	21311.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3476

GPRRVELDADATSGAFYARYRDGYVSGEPWPGAGPPPPGRVLYGGLGDSRPGLWGAPEAEEARRRFEASGAPAAVWAPELGDAAQQYALITRLLYTPDAEAMGWLQNPRVVPGDVALDQACFRISGAARNSSSFITGSVARAVPHLGYAMAAGRFGWGLAHAAAAVAMSRRYDRAQKGFLLTSLRRAYAPLLARENAALTG

Source Source

Source organism organism	Human herpesvirus 1 (strain 17)
Common name common_name	HHV-1
NCBI taxonomy ID ncbi_taxonomy_id	10299
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(PCPGPAPTPCPGPTPCP*C)-3') ;
Molecular weight formula_weight	3583.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

CCGATCGTCCAC

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(PCPGPAPTPCPGPTPCP*C)-3') ;
Molecular weight formula_weight	3743.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

GTGGACGATCGG

Entity 4 Entity 4 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	196

▶

Unit-cell length a length_a	127.254 Å
Unit-cell length b length_b	39.084 Å
Unit-cell length c length_c	90.443 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.117 Å
Low-resolution limit resolution_low	45.220 Å
R factor r_factor	0.1988
R_work r_work	0.1968
R_free r_free	0.2354

ICP4 DNA-binding domain, lacking intrinsically disordered region, in complex with 12mer DNA duplex from its own promoter

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

Major viral transcription factor ICP4

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

5mhj__assembly_1__model_1

5mhj__assembly_1__model_1 | I(q)

5mhj__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

ICP4 DNA-binding domain, lacking intrinsically disordered region, in complex with 12mer DNA duplex from its own promoter

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

Major viral transcription factor ICP4

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

5mhj__assembly_1__model_1

5mhj__assembly_1__model_1 | I(q)

5mhj__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)