SAXSdb — 5xsk

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

Hepatoma-derived growth factor

Rattus norvegicus

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(PTPTPCPAPAPGPAPCPCPA)-3') ; × 1 ;DNA (5'-D(PTPGPGPTPCPTPTPGPAPA)-3') ; × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HDGF_RAT
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 21–120； UniProt 1–100 Author chain B； PDBConstruct 21–120； UniProt 1–100

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	5xsk
Deposition date deposition_date	2017-06-14
Structure title title	Crystal structure of PWWP-DNA complex for human hepatoma-derived growth factor
Keywords keywords	Growth factor, HORMONE; HORMONE
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.

5xsk__assembly_1__model_1

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

Download this curve (.dat)

5xsk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5xsk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.50 Å
Rg (electron density)	27.18 Å
Total Rg	27.67 Å
Atom count	1903
Residues	201
Excluded volume	32762 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5xsk__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(PTPTPCPAPAPGPAPCPCPA)-3') ;
Molecular weight formula_weight	3013.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D
Atom count atom_count	1903

TTCAAGACCA

Source Source

Source organism organism	Escherichia coli BL21
NCBI taxonomy ID ncbi_taxonomy_id	511693
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(PTPGPGPTPCPTPTPGPAPA)-3') ;
Molecular weight formula_weight	3075.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

TGGTCTTGAA

Source Source

Source organism organism	Escherichia coli BL21
NCBI taxonomy ID ncbi_taxonomy_id	511693
Host organism host_organism	Escherichia coli BL21

Entity 3 Entity 3 polymer

Description description	Hepatoma-derived growth factor
Molecular weight formula_weight	13735.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

MGSSHHHHHHSSGLVPRGSHMSRSNRQKEYKCGDLVFAKMKGYPHWPARIDEMPEAAVKSTANKYQVFFFGTHETAFLGPKDLFPYEESKEKFGKPNKRKGFSEGLWEIENNPTVKASGY

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli BL21

Entity 4 Entity 4 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5xska_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.2 — PWWP domain

Domain ID domain_id	d5xskb_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.2 — PWWP domain

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Unit-cell length a length_a	32.402 Å
Unit-cell length b length_b	32.402 Å
Unit-cell length c length_c	205.820 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	2.840 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1952
R_work r_work	0.1911
R_free r_free	0.2692

Crystal structure of PWWP-DNA complex for human hepatoma-derived growth factor

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

Hepatoma-derived growth factor

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

5xsk__assembly_1__model_1

5xsk__assembly_1__model_1 | I(q)

5xsk__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)

Crystal structure of PWWP-DNA complex for human hepatoma-derived growth factor

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

Hepatoma-derived growth factor

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

5xsk__assembly_1__model_1

5xsk__assembly_1__model_1 | I(q)

5xsk__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)