SAXSdb — 8xam

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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	S-ADENOSYLMETHIONINE × 2 ;2-[3-[7-chloranyl-4-(dimethylamino)-2-oxidanylidene-quinazolin-1-yl]phenoxy]-~{N}-[3-[7-chloranyl-4-(dimethylamino)-2-oxidanylidene-quinazolin-1-yl]phenyl]ethanamide ; × 1 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 1–380； UniProt 16–395 Author chain B； PDBConstruct 1–380； UniProt 16–395

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	8xam
Deposition date deposition_date	2023-12-04
Structure title title	Co-crystal structure of compound 7 in complex with MAT2A
Keywords keywords	MAT2A inhibitor, 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.

8xam__assembly_1__model_1

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

Download this curve (.dat)

8xam__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8xam__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.52 Å
Rg (electron density)	24.34 Å
Total Rg	25.34 Å
Atom count	5983
Residues	760
Excluded volume	106260 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8xam__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 (4)

Entity 1 Entity 1 polymer

Description description	S-adenosylmethionine synthase isoform type-2
Molecular weight formula_weight	42001.8 kDa
EC 编号 ec_number	2.5.1.6
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	7264

GTFLFTSESVGEGHPDKICDQISDAVLDAHLQQDPDAKVACETVAKTGMILLAGEITSRAAVDYQKVVREAVKHIGYDDSSKGFDYKTCNVLVALEQQSPDIAQGVHLDRNEEDIGAGDQGLMFGYATDETEECMPLTIVLAHKLNAKLAELRRNGTLPWLRPDSKTQVTVQYMQDRGAVLPIRVHTIVISVQHDEEVCLDEMRDALKEKVIKAVVPAKYLDEDTIYHLQPSGRFVIGGPQGDAGLTGRKIIVDTYGGWGAHGGGAFSGKDYTKVDRSAAYAARWVAKSLVKGGLCRRVLVQVSYAIGVSHPLSISIFHYGTSQKSERELLEIVKKNFDLRPGVIVRDLDLKKPIYQRTAAYGHFGRDSFPWEVPKKLKY

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia phage EcWhh-1

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	;2-[3-[7-chloranyl-4-(dimethylamino)-2-oxidanylidene-quinazolin-1-yl]phenoxy]-~{N}-[3-[7-chloranyl-4-(dimethylamino)-2-oxidanylidene-quinazolin-1-yl]phenyl]ethanamide ;
Molecular weight formula_weight	670.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1098

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Unit-cell length a length_a	67.968 Å
Unit-cell length b length_b	94.043 Å
Unit-cell length c length_c	116.892 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 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	40.119 Å
R factor r_factor	—
R_work r_work	0.1213
R_free r_free	0.1427

Co-crystal structure of compound 7 in complex with MAT2A

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

8xam__assembly_1__model_1

8xam__assembly_1__model_1 | I(q)

8xam__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

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Co-crystal structure of compound 7 in complex with MAT2A

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

8xam__assembly_1__model_1

8xam__assembly_1__model_1 | I(q)

8xam__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

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)