3thr

Crystal structure of rat native liver Glycine N-methyltransferase complexed with 5-methyltetrahydrofolate monoglutamate

Method: X-RAY DIFFRACTION

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

Glycine N-methyltransferase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID × 4 TRIS(HYDROXYETHYL)AMINOMETHANE × 3 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GNMT_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–293； UniProt 2–293 Author chain B； PDBConstruct 2–293； UniProt 2–293 Author chain C； PDBConstruct 2–293； UniProt 2–293 Author chain D； PDBConstruct 2–293； 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	3thr
Deposition date deposition_date	2011-08-19
Structure title title	Crystal structure of rat native liver Glycine N-methyltransferase complexed with 5-methyltetrahydrofolate monoglutamate
Keywords keywords	;Glycine N-methyltransferase, GNMT, Folate, methyltransferase, Folate Binding, Liver cytosol, Transferase-Transferase Inhibitor complex ;; Transferase/Transferase Inhibitor
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.

3thr__assembly_1__model_1

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

Download this curve (.dat)

3thr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3thr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.72 Å
Rg (electron density)	35.05 Å
Total Rg	35.59 Å
Atom count	9149
Residues	1141
Excluded volume	162380 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3thr__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	Glycine N-methyltransferase
Molecular weight formula_weight	32486.9 kDa
EC 编号 ec_number	2.1.1.20
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9887

XVDSVYRTRSLGVAAEGIPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVEEGFSVTSVDASDKMLKYALKERWNRRKEPAFDKWVIEEANWLTLDKDVPAGDGFDAVICLGNSFAHLPDSKGDQSEHRLALKNIASMVRPGGLLVIDHRNYDYILSTGCAPPGKNIYYKSDLTKDITTSVLTVNNKAHMVTLDYTVQVPGAGRDGAPGFSKFRLSYYPHCLASFTELVQEAFGGRCQHSVLGDFKPYRPGQAYVPCYFIHVLKKTG

Entity 2 Entity 2 non-polymer

Description description	5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID
Molecular weight formula_weight	459.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	TRIS(HYDROXYETHYL)AMINOMETHANE
Molecular weight formula_weight	163.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	725

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3thra_
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	d3thrb_
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	d3thrc_
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	d3thrd_
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 (8 domains)

Domain ID domain_id	3thrA01
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	3thrA02
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	3thrB01
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	3thrB02
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	3thrC01
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	3thrC02
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	3thrD01
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	3thrD02
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	59.186 Å
Unit-cell length b length_b	83.788 Å
Unit-cell length c length_c	134.436 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.32 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	31.190 Å
R factor r_factor	0.1811
R_work r_work	0.1781
R_free r_free	0.2407

Crystal structure of rat native liver Glycine N-methyltransferase complexed with 5-methyltetrahydrofolate monoglutamate

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

3thr__assembly_1__model_1

3thr__assembly_1__model_1 | I(q)

3thr__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

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of rat native liver Glycine N-methyltransferase complexed with 5-methyltetrahydrofolate monoglutamate

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

3thr__assembly_1__model_1

3thr__assembly_1__model_1 | I(q)

3thr__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

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)