7kdb

Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric inhibitor compound 35

Method: X-RAY DIFFRACTION

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

S-adenosylmethionine synthase isoform type-2

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	6-(4-hydroxyphenyl)-2,3-diphenyl-5-[(1H-pyrazol-3-yl)amino]pyrazolo[1,5-a]pyrimidin-7(4H)-one × 2 CHLORIDE ION × 4 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 1,2-ETHANEDIOL × 6 GLYCEROL × 2 S-ADENOSYLMETHIONINE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	METK2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–396； UniProt 1–395

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	7kdb
Deposition date deposition_date	2020-10-08
Structure title title	Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric inhibitor compound 35
Keywords keywords	ETHIONINE ADENOSYLTRANSFERASE, SAM, Allosteric Inhibitor, TRANSFERASE, TRANSFERASE-Inhibitor complex; 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.

7kdb__assembly_1__model_1

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

Download this curve (.dat)

7kdb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7kdb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.71 Å
Rg (electron density)	24.51 Å
Total Rg	25.54 Å
Atom count	12126
Residues	762
Excluded volume	108470 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7kdb__assembly_1__model_1`	dimeric （2）	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 (8)

Entity 1 Entity 1 polymer

Description description	S-adenosylmethionine synthase isoform type-2
Molecular weight formula_weight	43807.7 kDa
EC 编号 ec_number	2.5.1.6
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7193

SMNGQLNGFHEAFIEEGTFLFTSESVGEGHPDKICDQISDAVLDAHLQQDPDAKVACETVAKTGMILLAGEITSRAAVDYQKVVREAVKHIGYDDSSKGFDYKTCNVLVALEQQSPDIAQGVHLDRNEEDIGAGDQGLMFGYATDETEECMPLTIVLAHKLNAKLAELRRNGTLPWLRPDSKTQVTVQYMQDRGAVLPIRVHTIVISVQHDEEVCLDEMRDALKEKVIKAVVPAKYLDEDTIYHLQPSGRFVIGGPQGDAGLTGRKIIVDTYGGWGAHGGGAFSGKDYTKVDRSAAYAARWVAKSLVKGGLCRRVLVQVSYAIGVSHPLSISIFHYGTSQKSERELLEIVKKNFDLRPGVIVRDLDLKKPIYQRTAAYGHFGRDSFPWEVPKKLKY

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	6-(4-hydroxyphenyl)-2,3-diphenyl-5-[(1H-pyrazol-3-yl)amino]pyrazolo[1,5-a]pyrimidin-7(4H)-one
Molecular weight formula_weight	460.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

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	3

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	1

Entity 7 Entity 7 non-polymer

Description description	S-ADENOSYLMETHIONINE
Molecular weight formula_weight	398.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	510

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d7kdba1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.130 — S-adenosylmethionine synthetase
Superfamily Superfamily superfamily	d.130.1 — S-adenosylmethionine synthetase
Family Family family	d.130.1.1 — S-adenosylmethionine synthetase

Domain ID domain_id	d7kdba2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.130 — S-adenosylmethionine synthetase
Superfamily Superfamily superfamily	d.130.1 — S-adenosylmethionine synthetase
Family Family family	d.130.1.1 — S-adenosylmethionine synthetase

Domain ID domain_id	d7kdba3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.130 — S-adenosylmethionine synthetase
Superfamily Superfamily superfamily	d.130.1 — S-adenosylmethionine synthetase
Family Family family	d.130.1.1 — S-adenosylmethionine synthetase

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Unit-cell length a length_a	68.110 Å
Unit-cell length b length_b	94.027 Å
Unit-cell length c length_c	116.795 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	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	orthorhombic

Resolution resolution	1.240 Å
Low-resolution limit resolution_low	30.880 Å
R factor r_factor	0.1270
R_work r_work	0.1264
R_free r_free	0.1384

Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric inhibitor compound 35

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

S-adenosylmethionine synthase isoform type-2

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

7kdb__assembly_1__model_1

7kdb__assembly_1__model_1 | I(q)

7kdb__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 (8)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

7. Citations (1)

Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric inhibitor compound 35

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

S-adenosylmethionine synthase isoform type-2

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

7kdb__assembly_1__model_1

7kdb__assembly_1__model_1 | I(q)

7kdb__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 (8)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

7. Citations (1)