6sw5

Crystal structure of the human S-adenosylmethionine synthetase 1 (ligand-free form)

Method: X-RAY DIFFRACTION

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

S-adenosylmethionine synthase isoform type-1

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	DI(HYDROXYETHYL)ETHER × 2 1,2-ETHANEDIOL × 8 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	1,2-ETHANEDIOL × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	METK1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–395； UniProt 1–395 Author chain B； PDBConstruct 1–395； UniProt 1–395 Author chain C； PDBConstruct 1–395； UniProt 1–395 Author chain D； PDBConstruct 1–395； 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	6sw5
Deposition date deposition_date	2019-09-19
Structure title title	Crystal structure of the human S-adenosylmethionine synthetase 1 (ligand-free form)
Keywords keywords	S-adenosylmethionine synthesis, 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.

6sw5__assembly_1__model_1

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

Download this curve (.dat)

6sw5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6sw5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.00 Å
Rg (electron density)	24.80 Å
Total Rg	25.81 Å
Atom count	5659
Residues	725
Excluded volume	100990 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6sw5__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6sw5__assembly_2__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-1
Molecular weight formula_weight	43703.9 kDa
EC 编号 ec_number	2.5.1.6
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	11679

MNGPVDGLCDHSLSEGVFMFTSESVGEGHPDKICDQISDAVLDAHLKQDPNAKVACETVCKTGMVLLCGEITSMAMVDYQRVVRDTIKHIGYDDSAKGFDFKTCNVLVALEQQSPDIAQCVHLDRNEEDVGAGDQGLMFGYATDETEECMPLTIILAHKLNARMADLRRSGLLPWLRPDSKTQVTVQYMQDNGAVIPVRIHTIVISVQHNEDITLEEMRRALKEQVIRAVVPAKYLDEDTVYHLQPSGRFVIGGPQGDAGVTGRKIIVDTYGGWGAHGGGAFSGKDYTKVDRSAAYAARWVAKSLVKAGLCRRVLVQVSYAIGVAEPLSISIFTYGTSQKTERELLDVVHKNFDLRPGVIVRDLDLKKPIYQKTACYGHFGRSEFPWEVPRKLVF

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	399

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d6sw5a1
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.130.1.0 — automated matches

Domain ID domain_id	d6sw5a2
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.130.1.0 — automated matches

Domain ID domain_id	d6sw5a3
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.130.1.0 — automated matches

Domain ID domain_id	d6sw5b1
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.130.1.0 — automated matches

Domain ID domain_id	d6sw5b2
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.130.1.0 — automated matches

Domain ID domain_id	d6sw5b3
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.130.1.0 — automated matches

Domain ID domain_id	d6sw5c1
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.130.1.0 — automated matches

Domain ID domain_id	d6sw5c2
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.130.1.0 — automated matches

Domain ID domain_id	d6sw5c3
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.130.1.0 — automated matches

Domain ID domain_id	d6sw5d1
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.130.1.0 — automated matches

Domain ID domain_id	d6sw5d2
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.130.1.0 — automated matches

Domain ID domain_id	d6sw5d3
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.130.1.0 — automated matches

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Unit-cell length a length_a	218.684 Å
Unit-cell length b length_b	61.000 Å
Unit-cell length c length_c	119.762 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.55 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	58.760 Å
R factor r_factor	0.1908
R_work r_work	0.1882
R_free r_free	0.2387

Crystal structure of the human S-adenosylmethionine synthetase 1 (ligand-free form)

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

S-adenosylmethionine synthase isoform type-1

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

6sw5__assembly_1__model_1

6sw5__assembly_1__model_1 | I(q)

6sw5__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

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

7. Citations (1)

Crystal structure of the human S-adenosylmethionine synthetase 1 (ligand-free form)

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

S-adenosylmethionine synthase isoform type-1

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

6sw5__assembly_1__model_1

6sw5__assembly_1__model_1 | I(q)

6sw5__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

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

7. Citations (1)