SAXSdb — 5tuz

▼

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

Histone-lysine N-methyltransferase EHMT1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	S-ADENOSYLMETHIONINE × 2 ZINC ION × 8 6,7-dimethoxy-N-(1-methylpiperidin-4-yl)-2-(morpholin-4-yl)quinazolin-4-amine × 2 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EHMT1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–261； UniProt 1006–1266 Author chain B； PDBConstruct 1–261； UniProt 1006–1266

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	5tuz
Deposition date deposition_date	2016-11-07
Structure title title	Structure of human GLP SET-domain (EHMT1) in complex with inhibitor MS0124
Keywords keywords	Methyl Transferase, Transferase-Transferase Inhibitor complex; Transferase/Transferase Inhibitor
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.

5tuz__assembly_1__model_1

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

Download this curve (.dat)

5tuz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5tuz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.23 Å
Rg (electron density)	25.37 Å
Total Rg	26.08 Å
Atom count	4300
Residues	516
Excluded volume	75592 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5tuz__assembly_1__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 (6)

Entity 1 Entity 1 polymer

Description description	Histone-lysine N-methyltransferase EHMT1
Molecular weight formula_weight	30232.4 kDa
EC 编号 ec_number	2.1.1.-,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,B
Atom count atom_count	4640

VERIVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSPMNIDRNITHLQYCVCIDDCSSSNCMCGQLSMRCWYDKDGRLLPEFNMAEPPLIFECNHACSCWRNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEYVGELISDSEADVREEDSYLFDLDNKDGEVYCIDARFYGNVSRFINHHCEPNLVPVRVFMAHQDLRFPRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLFSCRCGSPKCRHS

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 non-polymer

Description description	S-ADENOSYLMETHIONINE
Molecular weight formula_weight	398.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	6,7-dimethoxy-N-(1-methylpiperidin-4-yl)-2-(morpholin-4-yl)quinazolin-4-amine
Molecular weight formula_weight	387.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	340

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5tuza_
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.85.7.0 — automated matches

Domain ID domain_id	d5tuzb_
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.85.7.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	5tuzA00
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	5tuzB00
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	74.940 Å
Unit-cell length b length_b	95.780 Å
Unit-cell length c length_c	102.360 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	1.950 Å
Low-resolution limit resolution_low	59.021 Å
R factor r_factor	0.1634
R_work r_work	0.1614
R_free r_free	0.2006

Structure of human GLP SET-domain (EHMT1) in complex with inhibitor MS0124

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

Histone-lysine N-methyltransferase EHMT1

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

5tuz__assembly_1__model_1

5tuz__assembly_1__model_1 | I(q)

5tuz__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of human GLP SET-domain (EHMT1) in complex with inhibitor MS0124

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

Histone-lysine N-methyltransferase EHMT1

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

5tuz__assembly_1__model_1

5tuz__assembly_1__model_1 | I(q)

5tuz__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)