1r8y

Crystal Structure of Mouse Glycine N-Methyltransferase (Monoclinic Form)

Method: X-RAY DIFFRACTION

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

glycine N-methyltransferase

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	BETA-MERCAPTOETHANOL × 6 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	BETA-MERCAPTOETHANOL × 4 water × 3	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 8	BETA-MERCAPTOETHANOL × 10 water × 5	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 8	BETA-MERCAPTOETHANOL × 10 water × 5	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 8	BETA-MERCAPTOETHANOL × 10 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GNMT_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–292； UniProt 2–293 Author chain B； PDBConstruct 1–292； UniProt 2–293 Author chain C； PDBConstruct 1–292； UniProt 2–293 Author chain D； PDBConstruct 1–292； UniProt 2–293 Author chain E； PDBConstruct 1–292； UniProt 2–293 Author chain F； PDBConstruct 1–292； UniProt 2–293 Author chain G； PDBConstruct 1–292； UniProt 2–293 Author chain H； PDBConstruct 1–292； UniProt 2–293

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	1r8y
Deposition date deposition_date	2003-10-28
Structure title title	Crystal Structure of Mouse Glycine N-Methyltransferase (Monoclinic Form)
Keywords keywords	Glycine N-Methyltransferase, TRANSFERASE; TRANSFERASE
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.

1r8y__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1r8y__assembly_5__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1r8y__assembly_5__model_1 | P(r) · Pending

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

Rg（Guinier）	52.57 Å
Rg (electron density)	52.62 Å
Total Rg	52.63 Å
Atom count	17592
Residues	2265
Excluded volume	311530 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1r8y__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1r8y__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1r8y__assembly_3__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1r8y__assembly_4__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1r8y__assembly_5__model_1`	octameric （8）	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 (3)

Entity 1 Entity 1 polymer

Description description	glycine N-methyltransferase
Molecular weight formula_weight	32587.0 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	17606

VDSVYRTRSLGVAAEGLPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVEEGFSVMSVDASDKMLKYALKERWNRRKEPSFDNWVIEEANWLTLDKDVLSGDGFDAVICLGNSFAHLPDCKGDQSEHRLALKNIASMVRPGGLLVIDHRNYDYILSTGCAPPGKNIYYKSDLTKDITTSVLTVNNKAHMVTLDYTVQVPGTGRDGSPGFSKFRLSYYPHCLASFTELVRAAFGGRCQHSVLGDFKPYKPGQAYVPCYFIHVLKKTD

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	14

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1r8ya_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.5 — Glycine N-methyltransferase

Domain ID domain_id	d1r8yb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.5 — Glycine N-methyltransferase

Domain ID domain_id	d1r8yc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.5 — Glycine N-methyltransferase

Domain ID domain_id	d1r8yd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.5 — Glycine N-methyltransferase

Domain ID domain_id	d1r8ye_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.5 — Glycine N-methyltransferase

Domain ID domain_id	d1r8yf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.5 — Glycine N-methyltransferase

Domain ID domain_id	d1r8yg_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.5 — Glycine N-methyltransferase

Domain ID domain_id	d1r8yh_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.5 — Glycine N-methyltransferase

CATH v4.4 (16 domains)

Domain ID domain_id	1r8yA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	46 — Glycine N-methyltransferase; chain A, domain 1
Homologous superfamily homologous superfamily	10 — Glycine N-methyltransferase, chain A, domain 1

Domain ID domain_id	1r8yA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	1r8yB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	46 — Glycine N-methyltransferase; chain A, domain 1
Homologous superfamily homologous superfamily	10 — Glycine N-methyltransferase, chain A, domain 1

Domain ID domain_id	1r8yB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	1r8yC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	46 — Glycine N-methyltransferase; chain A, domain 1
Homologous superfamily homologous superfamily	10 — Glycine N-methyltransferase, chain A, domain 1

Domain ID domain_id	1r8yC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	1r8yD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	46 — Glycine N-methyltransferase; chain A, domain 1
Homologous superfamily homologous superfamily	10 — Glycine N-methyltransferase, chain A, domain 1

Domain ID domain_id	1r8yD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	1r8yE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	46 — Glycine N-methyltransferase; chain A, domain 1
Homologous superfamily homologous superfamily	10 — Glycine N-methyltransferase, chain A, domain 1

Domain ID domain_id	1r8yE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	1r8yF01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	46 — Glycine N-methyltransferase; chain A, domain 1
Homologous superfamily homologous superfamily	10 — Glycine N-methyltransferase, chain A, domain 1

Domain ID domain_id	1r8yF02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	1r8yG01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	46 — Glycine N-methyltransferase; chain A, domain 1
Homologous superfamily homologous superfamily	10 — Glycine N-methyltransferase, chain A, domain 1

Domain ID domain_id	1r8yG02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	1r8yH01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	46 — Glycine N-methyltransferase; chain A, domain 1
Homologous superfamily homologous superfamily	10 — Glycine N-methyltransferase, chain A, domain 1

Domain ID domain_id	1r8yH02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

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Unit-cell length a length_a	107.980 Å
Unit-cell length b length_b	108.300 Å
Unit-cell length c length_c	119.010 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.71 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	13.000 Å
R factor r_factor	0.2240
R_work r_work	0.2221
R_free r_free	0.2851

Crystal Structure of Mouse Glycine N-Methyltransferase (Monoclinic Form)

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

glycine N-methyltransferase

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

1r8y__assembly_5__model_1

1r8y__assembly_5__model_1 | I(q)

1r8y__assembly_5__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (8 domains)

CATH v4.4 (16 domains)

7. Citations (1)

Crystal Structure of Mouse Glycine N-Methyltransferase (Monoclinic Form)

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

glycine N-methyltransferase

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

1r8y__assembly_5__model_1

1r8y__assembly_5__model_1 | I(q)

1r8y__assembly_5__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (8 domains)

CATH v4.4 (16 domains)

7. Citations (1)