6faj

The structure of Human Methionine Adenosyltransferase II in apo state

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 4	DI(HYDROXYETHYL)ETHER × 4 TETRAETHYLENE GLYCOL × 2 ACETATE ION × 2 water × 4	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 1–395； UniProt 1–395 Author chain B； 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	6faj
Deposition date deposition_date	2017-12-15
Structure title title	The structure of Human Methionine Adenosyltransferase II in apo state
Keywords keywords	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.

6faj__assembly_1__model_1

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

Download this curve (.dat)

6faj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6faj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.21 Å
Rg (electron density)	36.11 Å
Total Rg	36.55 Å
Atom count	11484
Residues	1482
Excluded volume	204610 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6faj__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 (5)

Entity 1 Entity 1 polymer

Description description	S-adenosylmethionine synthase isoform type-2
Molecular weight formula_weight	43720.6 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	6044

MNGQLNGFHEAFIEEGTFLFTSESVGEGHPDKICDQISDAVLDAHLQQDPDAKVACETVAKTGMILLAGEITSRAAVDYQKVVREAVKHIGYDDSSKGFDYKTCNVLVALEQQSPDIAQGVHLDRNEEDIGAGDQGLMFGYATDETEECMPLTIVLAHKLNAKLAELRRNGTLPWLRPDSKTQVTVQYMQDRGAVLPIRVHTIVISVQHDEEVCLDEMRDALKEKVIKAVVPAKYLDEDTIYHLQPSGRFVIGGPQGDAGLTGRKIIVDTYGGWGAHGGGAFSGKDYTKVDRSAAYAARWVAKSLVKGGLCRRVLVQVSYAIGVSHPLSISIFHYGTSQKSERELLEIVKKNFDLRPGVIVRDLDLKKPIYQRTAAYGHFGRDSFPWEVPKKLKY

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	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	302

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d6faja1
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	d6faja2
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	d6faja3
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	d6fajb1
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	d6fajb2
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	d6fajb3
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

CATH v4.4 (6 domains)

Domain ID domain_id	6fajA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	6fajA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	6fajA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	6fajB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	6fajB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	6fajB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	62.176 Å
Unit-cell length b length_b	103.232 Å
Unit-cell length c length_c	108.359 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	P 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	74.740 Å
R factor r_factor	0.1915
R_work r_work	0.1896
R_free r_free	0.2239

The structure of Human Methionine Adenosyltransferase II in apo state

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

6faj__assembly_1__model_1

6faj__assembly_1__model_1 | I(q)

6faj__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

The structure of Human Methionine Adenosyltransferase II in apo state

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

6faj__assembly_1__model_1

6faj__assembly_1__model_1 | I(q)

6faj__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)