4i51

Methyltransferase domain of HUMAN EUCHROMATIC HISTONE METHYLTRANSFERASE 1, mutant Y1211A

Method: X-RAY DIFFRACTION

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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 heterocomplex	Heteromer	Protein 5	H3K9 NE-ALLYL PEPTIDE × 2 UNKNOWN PEPTIDE × 1 S-ADENOSYL-L-HOMOCYSTEINE × 2 ZINC ION × 8 GLYCEROL × 3 UNKNOWN ATOM OR ION × 9 water × 4	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 2–286； UniProt 982–1266 Author chain B； PDBConstruct 2–286； UniProt 982–1266

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4i51
Deposition date deposition_date	2012-11-28
Structure title title	Methyltransferase domain of HUMAN EUCHROMATIC HISTONE METHYLTRANSFERASE 1, mutant Y1211A
Keywords keywords	NE-ALLYL PEPTIDE, STRUCTURAL GENOMICS CONSORTIUM, Transferase-Peptide complex, SGC; Transferase/Peptide
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.

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4i51__assembly_1__model_1`	pentameric （5）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Histone-lysine N-methyltransferase EHMT1
Molecular weight formula_weight	32795.2 kDa
EC 编号 ec_number	2.1.1.-, 2.1.1.43
Mutation mutation	Y1211A
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	5000

GNSQVWSALQMSKALQDSAPDRPSPVERIVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSPMNIDRNITHLQYCVCIDDCSSSNCMCGQLSMRCWYDKDGRLLPEFNMAEPPLIFECNHACSCWRNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEYVGELISDSEADVREEDSYLFDLDNKDGEVYCIDARFYGNVSRFINHHCEPNLVPVRVFMAHQDLRFPRIAFFSTRLIEAGEQLGFDAGERFWDIKGKLFSCRCGSPKCRHS

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	H3K9 NE-ALLYL PEPTIDE
Molecular weight formula_weight	1050.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

TKQTARKST

Entity 3 Entity 3 polymer

Description description	UNKNOWN PEPTIDE
Molecular weight formula_weight	1124.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

XXXXXXXXXXXXX

Entity 4 Entity 4 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 5 Entity 5 non-polymer

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

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	UNKNOWN ATOM OR ION
Source method src_method	syn
Copy count entity_count	9

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	503

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4i51A00
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	4i51B00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	270 — Beta-clip-like
Homologous superfamily homologous superfamily	10 — SET domain

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Unit-cell length a length_a	83.497 Å
Unit-cell length b length_b	83.800 Å
Unit-cell length c length_c	95.052 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	1.900 Å
Low-resolution limit resolution_low	41.780 Å
R factor r_factor	0.1710
R_work r_work	0.1710
R_free r_free	0.1950

Methyltransferase domain of HUMAN EUCHROMATIC HISTONE METHYLTRANSFERASE 1, mutant Y1211A

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

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Methyltransferase domain of HUMAN EUCHROMATIC HISTONE METHYLTRANSFERASE 1, mutant Y1211A

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

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)