SAXSdb — 1xqh

▼

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

Histone-lysine N-methyltransferase, H3 lysine-4 specific

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	9-mer peptide from tumor protein p53 × 1 （P04637） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	9-mer peptide from tumor protein p53 × 1 （P04637） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SET7_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–264； UniProt 108–366 Author chain E； PDBConstruct 6–264； UniProt 108–366

9-mer peptide from tumor protein p53

OrganismNot specified

UniProt P04637

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Histone-lysine N-methyltransferase, H3 lysine-4 specific × 1 （Q8WTS6） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Histone-lysine N-methyltransferase, H3 lysine-4 specific × 1 （Q8WTS6） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P53_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–9； UniProt 369–377 Author chain F； PDBConstruct 1–9； UniProt 369–377

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	1xqh
Deposition date deposition_date	2004-10-12
Structure title title	Crystal structure of a ternary complex of the methyltransferase SET9 (also known as SET7/9) with a P53 peptide and SAH
Keywords keywords	Set9-p53 complex, Set-domain, Lysine methylation, TRANSFERASE; TRANSFERASE
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.

1xqh__assembly_1__model_1

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

Download this curve (.dat)

1xqh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1xqh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.49 Å
Rg (electron density)	19.49 Å
Total Rg	20.47 Å
Atom count	2026
Residues	255
Excluded volume	35713 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1xqh__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1xqh__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Histone-lysine N-methyltransferase, H3 lysine-4 specific
Molecular weight formula_weight	29323.6 kDa
EC 编号 ec_number	2.1.1.43
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	4771

GPLGSGQYKDNIRHGVCWIYYPDGGSLVGEVNEDGEMTGEKIAYVYPDERTALYGKFIDGEMIEGKLATLMSTEEGRPHFELMPGNSVYHFDKSTSSCISTNALLPDPYESERVYVAESLISSAGEGLFSKVAVGPNTVMSFYNGVRITHQEVDSRDWALNGNTLSLDEETVIDVPEPYNHVSKYCASLGHKANHSFTPNCIYDMFVHPRFGPIKCIRTLRAVEADEELTVAYGYDHSPPGKSGPEAPEWYQVELKAFQATQQK

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	9-mer peptide from tumor protein p53
Molecular weight formula_weight	1155.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

LKSKKGQSTY

Entity 3 Entity 3 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	717

▼

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1xqha1
Class class	b — All beta proteins
Fold Fold fold	b.76 — open-sided beta-meander
Superfamily Superfamily superfamily	b.76.2 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
Family Family family	b.76.2.1 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain

Domain ID domain_id	d1xqha2
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.7 — SET domain
Family Family family	b.85.7.1 — Histone lysine methyltransferases

Domain ID domain_id	d1xqhe1
Class class	b — All beta proteins
Fold Fold fold	b.76 — open-sided beta-meander
Superfamily Superfamily superfamily	b.76.2 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
Family Family family	b.76.2.1 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain

Domain ID domain_id	d1xqhe2
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.7 — SET domain
Family Family family	b.85.7.1 — Histone lysine methyltransferases

CATH v4.4 (4 domains)

Domain ID domain_id	1xqhA01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	110 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
Homologous superfamily homologous superfamily	10 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain

Domain ID domain_id	1xqhA02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	270 — Beta-clip-like
Homologous superfamily homologous superfamily	10 — SET domain

Domain ID domain_id	1xqhE01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	110 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
Homologous superfamily homologous superfamily	10 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain

Domain ID domain_id	1xqhE02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	270 — Beta-clip-like
Homologous superfamily homologous superfamily	10 — SET domain

▶

Unit-cell length a length_a	40.374 Å
Unit-cell length b length_b	103.123 Å
Unit-cell length c length_c	67.165 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.04 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1857
R_work r_work	0.1837
R_free r_free	0.2233

Crystal structure of a ternary complex of the methyltransferase SET9 (also known as SET7/9) with a P53 peptide and SAH

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

Histone-lysine N-methyltransferase, H3 lysine-4 specific

State in the Current Structure

Other States of the Same Protein in the Database

9-mer peptide from tumor protein p53

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

1xqh__assembly_1__model_1

1xqh__assembly_1__model_1 | I(q)

1xqh__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

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of a ternary complex of the methyltransferase SET9 (also known as SET7/9) with a P53 peptide and SAH

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

Histone-lysine N-methyltransferase, H3 lysine-4 specific

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

9-mer peptide from tumor protein p53

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

1xqh__assembly_1__model_1

1xqh__assembly_1__model_1 | I(q)

1xqh__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

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)