5a0y

METHYL-COENZYME M REDUCTASE FROM METHANOTHERMOBACTER MARBURGENSIS AT 1.1 A RESOLUTION

Method: X-RAY DIFFRACTION

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

METHYL-COENZYME M REDUCTASE I SUBUNIT ALPHA

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	METHYL-COENZYME M REDUCTASE I SUBUNIT BETA × 2 （P11560） METHYL-COENZYME M REDUCTASE I SUBUNIT GAMMA × 2 （P11562） MAGNESIUM ION × 16 FACTOR 430 × 2 1-THIOETHANESULFONIC ACID × 2 Coenzyme B × 2 POTASSIUM ION × 1 SODIUM ION × 2 CHLORIDE ION × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MCRA_METTM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–550； UniProt 1–550 Author chain D； PDBConstruct 1–550； UniProt 1–550

METHYL-COENZYME M REDUCTASE I SUBUNIT BETA

OrganismNot specified

UniProt P11560

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	METHYL-COENZYME M REDUCTASE I SUBUNIT ALPHA × 2 （P11558） METHYL-COENZYME M REDUCTASE I SUBUNIT GAMMA × 2 （P11562） MAGNESIUM ION × 16 FACTOR 430 × 2 1-THIOETHANESULFONIC ACID × 2 Coenzyme B × 2 POTASSIUM ION × 1 SODIUM ION × 2 CHLORIDE ION × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MCRB_METTM
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–443； UniProt 1–443 Author chain E； PDBConstruct 1–443； UniProt 1–443

METHYL-COENZYME M REDUCTASE I SUBUNIT GAMMA

OrganismNot specified

UniProt P11562

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	METHYL-COENZYME M REDUCTASE I SUBUNIT ALPHA × 2 （P11558） METHYL-COENZYME M REDUCTASE I SUBUNIT BETA × 2 （P11560） MAGNESIUM ION × 16 FACTOR 430 × 2 1-THIOETHANESULFONIC ACID × 2 Coenzyme B × 2 POTASSIUM ION × 1 SODIUM ION × 2 CHLORIDE ION × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MCRG_METTM
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–249； UniProt 1–249 Author chain F； PDBConstruct 1–249； UniProt 1–249

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	5a0y
Deposition date deposition_date	2015-04-24
Structure title title	METHYL-COENZYME M REDUCTASE FROM METHANOTHERMOBACTER MARBURGENSIS AT 1.1 A RESOLUTION
Keywords keywords	;TRANSFERASE, POST-TRANSLATIONAL MODIFICATION, BINDING SITES, CATALYSIS, COENZYMES, DISULFIDES, HYDROGEN, HYDROGEN BONDING, LIGANDS, MESNA, METALLOPORPHYRINS, METHANE, METHANOBACTERIUM, MODELS, MOLECULAR, NICKEL, OXIDATION-REDUCTION, OXIDOREDUCTASES, PHOSPHOTHREONINE, PROTEIN CONFORMATION, PROTEIN FOLDING, PROTEIN STRUCTURE ;; 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.

5a0y__assembly_1__model_1

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

Download this curve (.dat)

5a0y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5a0y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.46 Å
Rg (electron density)	37.58 Å
Total Rg	38.01 Å
Atom count	19336
Residues	2465
Excluded volume	342400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5a0y__assembly_1__model_1`	hexameric （6）	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 (11)

Entity 1 Entity 1 polymer

Description description	METHYL-COENZYME M REDUCTASE I SUBUNIT ALPHA
Molecular weight formula_weight	60637.6 kDa
EC 编号 ec_number	2.8.4.1
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	22747

MADKLFINALKKKFEESPEEKKTTFYTLGGWKQSERKTEFVNAGKEVAAKRGIPQYNPDIGTPLGQRVLMPYQVSTTDTYVEGDDLHFVNNAAMQQMWDDIRRTVIVGLNHAHAVIEKRLGKEVTPETITHYLETVNHAMPGAAVVQEHMVETHPALVADSYVKVFTGNDEIADEIDPAFVIDINKQFPEDQAETLKAEVGDGIWQVVRIPTIVSRTCDGATTSRWSAMQIGMSMISAYKQAAGEAATGDFAYAAKHAEVIHMGTYLPVRRARGENEPGGVPFGYLADICQSSRVNYEDPVRVSLDVVATGAMLYDQIWLGSYMSGGVGFTQYATAAYTDNILDDFTYFGKEYVEDKYGLCEAPNNMDTVLDVATEVTFYGLEQYEEYPALLEDQFGGSQRAAVVAAAAGCSTAFATGNAQTGLSGWYLSMYLHKEQHSRLGFYGYDLQDQCGASNVFSIRGDEGLPLELRGPNYPNYAMNVGHQGEYAGISQAPHAARGDAFVFNPLVKIAFADDNLVFDFTNVRGEFAKGALREFEPAGERALITPAK

Entity 2 Entity 2 polymer

Description description	METHYL-COENZYME M REDUCTASE I SUBUNIT BETA
Molecular weight formula_weight	47279.7 kDa
EC 编号 ec_number	2.8.4.1
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

MAKFEDKVDLYDDRGNLVEEQVPLEALSPLRNPAIKSIVQGIKRTVAVNLEGIENALKTAKVGGPACKIMGRELDLDIVGNAESIAAAAKEMIQVTEDDDTNVELLGGGKRALVQVPSARFDVAAEYSAAPLVTATAFVQAIINEFDVSMYDANMVKAAVLGRYPQSVEYMGANIATMLDIPQKLEGPGYALRNIMVNHVVAATLKNTLQAAALSTILEQTAMFEMGDAVGAFERMHLLGLAYQGMNADNLVFDLVKANGKEGTVGSVIADLVERALEDGVIKVEKELTDYKVYGTDDLAMWNAYAAAGLMAATMVNQGAARAAQGVSSTLLYYNDLIEFETGLPSVDFGKVEGTAVGFSFFSHSIYGGGGPGIFNGNHIVTRHSKGFAIPCVAAAMALDAGTQMFSPEATSGLIKEVFSQVDEFREPLKYVVEAAAEIKNEI

Entity 3 Entity 3 polymer

Description description	METHYL-COENZYME M REDUCTASE I SUBUNIT GAMMA
Molecular weight formula_weight	28797.2 kDa
EC 编号 ec_number	2.8.4.1
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

MAQYYPGTTKVAQNRRNFCNPEYELEKLREISDEDVVKILGHRAPGEEYPSVHPPLEEMDEPEDAIREMVEPIDGAKAGDRVRYIQFTDSMYFAPAQPYVRSRAYLCRYRGADAGTLSGRQIIETRERDLEKISKELLETEFFDPARSGVRGKSVHGHSLRLDEDGMMFDMLRRQIYNKDTGRVEMVKNQIGDELDEPVDLGEPLDEETLMEKTTIYRVDGEAYRDDVEAVEIMQRIHVLRSQGGFNLE

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 5 Entity 5 non-polymer

Description description	FACTOR 430
Molecular weight formula_weight	906.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	1-THIOETHANESULFONIC ACID
Molecular weight formula_weight	142.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	Coenzyme B
Molecular weight formula_weight	343.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

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

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2794

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6. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d5a0ya1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.31 — Methyl-coenzyme M reductase subunits
Family Family family	d.58.31.2 — Methyl-coenzyme M reductase alpha and beta chain N-terminal domain

Domain ID domain_id	d5a0ya2
Class class	a — All alpha proteins
Fold Fold fold	a.89 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
Superfamily Superfamily superfamily	a.89.1 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
Family Family family	a.89.1.1 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain

Domain ID domain_id	d5a0yb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.31 — Methyl-coenzyme M reductase subunits
Family Family family	d.58.31.2 — Methyl-coenzyme M reductase alpha and beta chain N-terminal domain

Domain ID domain_id	d5a0yb2
Class class	a — All alpha proteins
Fold Fold fold	a.89 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
Superfamily Superfamily superfamily	a.89.1 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
Family Family family	a.89.1.1 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain

Domain ID domain_id	d5a0yc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.31 — Methyl-coenzyme M reductase subunits
Family Family family	d.58.31.1 — Methyl-coenzyme M reductase gamma chain

Domain ID domain_id	d5a0yd1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.31 — Methyl-coenzyme M reductase subunits
Family Family family	d.58.31.2 — Methyl-coenzyme M reductase alpha and beta chain N-terminal domain

Domain ID domain_id	d5a0yd2
Class class	a — All alpha proteins
Fold Fold fold	a.89 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
Superfamily Superfamily superfamily	a.89.1 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
Family Family family	a.89.1.1 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain

Domain ID domain_id	d5a0ye1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.31 — Methyl-coenzyme M reductase subunits
Family Family family	d.58.31.2 — Methyl-coenzyme M reductase alpha and beta chain N-terminal domain

Domain ID domain_id	d5a0ye2
Class class	a — All alpha proteins
Fold Fold fold	a.89 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
Superfamily Superfamily superfamily	a.89.1 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
Family Family family	a.89.1.1 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain

Domain ID domain_id	d5a0yf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.31 — Methyl-coenzyme M reductase subunits
Family Family family	d.58.31.1 — Methyl-coenzyme M reductase gamma chain

CATH v4.4 (12 domains)

Domain ID domain_id	5a0yA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	390 — Methyl-coenzyme M Reductase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Methyl-coenzyme M Reductase; Chain A, domain 1

Domain ID domain_id	5a0yA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	470 —

Domain ID domain_id	5a0yA03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	840 — Methyl-coenzyme M Reductase; Chain B, domain 2
Homologous superfamily homologous superfamily	10 — Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal

Domain ID domain_id	5a0yB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	840 — Methyl-coenzyme M Reductase; Chain B, domain 2
Homologous superfamily homologous superfamily	10 — Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal

Domain ID domain_id	5a0yB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	470 —

Domain ID domain_id	5a0yC00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	320 — Lambda Exonuclease; Chain A
Homologous superfamily homologous superfamily	20 — Methyl-coenzyme M reductase, gamma subunit

Domain ID domain_id	5a0yD01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	390 — Methyl-coenzyme M Reductase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Methyl-coenzyme M Reductase; Chain A, domain 1

Domain ID domain_id	5a0yD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	470 —

Domain ID domain_id	5a0yD03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	840 — Methyl-coenzyme M Reductase; Chain B, domain 2
Homologous superfamily homologous superfamily	10 — Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal

Domain ID domain_id	5a0yE01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	840 — Methyl-coenzyme M Reductase; Chain B, domain 2
Homologous superfamily homologous superfamily	10 — Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal

Domain ID domain_id	5a0yE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	470 —

Domain ID domain_id	5a0yF00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	320 — Lambda Exonuclease; Chain A
Homologous superfamily homologous superfamily	20 — Methyl-coenzyme M reductase, gamma subunit

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Unit-cell length a length_a	82.227 Å
Unit-cell length b length_b	118.300 Å
Unit-cell length c length_c	122.560 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.90 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.100 Å
Low-resolution limit resolution_low	48.346 Å
R factor r_factor	0.1117
R_work r_work	0.1107
R_free r_free	0.1291

METHYL-COENZYME M REDUCTASE FROM METHANOTHERMOBACTER MARBURGENSIS AT 1.1 A RESOLUTION

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

METHYL-COENZYME M REDUCTASE I SUBUNIT ALPHA

State in the Current Structure

Other States of the Same Protein in the Database

METHYL-COENZYME M REDUCTASE I SUBUNIT BETA

State in the Current Structure

Other States of the Same Protein in the Database

METHYL-COENZYME M REDUCTASE I SUBUNIT GAMMA

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

5a0y__assembly_1__model_1

5a0y__assembly_1__model_1 | I(q)

5a0y__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 (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer 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 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 water

6. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (10 domains)

CATH v4.4 (12 domains)

7. Citations (1)

METHYL-COENZYME M REDUCTASE FROM METHANOTHERMOBACTER MARBURGENSIS AT 1.1 A RESOLUTION

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

METHYL-COENZYME M REDUCTASE I SUBUNIT ALPHA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

METHYL-COENZYME M REDUCTASE I SUBUNIT BETA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

METHYL-COENZYME M REDUCTASE I SUBUNIT GAMMA

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

5a0y__assembly_1__model_1

5a0y__assembly_1__model_1 | I(q)

5a0y__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 (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer 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 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 water

6. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (10 domains)

CATH v4.4 (12 domains)

7. Citations (1)