1e6y

Methyl-coenzyme M reductase from Methanosarcina barkeri

Method: X-RAY DIFFRACTION

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

METHYL-COENZYME M REDUCTASE 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 BETA SUBUNIT × 2 （P07955） METHYL-COENZYME M REDUCTASE SUBUNIT GAMMA × 2 （P07964） FACTOR 430 × 2 Coenzyme B × 2 1-THIOETHANESULFONIC ACID × 2 GLYCEROL × 3 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MCRA_METBA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–569； UniProt 1–569 Author chain D； PDBConstruct 1–569； UniProt 1–569

METHYL-COENZYME M REDUCTASE I BETA SUBUNIT

OrganismNot specified

UniProt P07955

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 SUBUNIT ALPHA × 2 （P07962） METHYL-COENZYME M REDUCTASE SUBUNIT GAMMA × 2 （P07964） FACTOR 430 × 2 Coenzyme B × 2 1-THIOETHANESULFONIC ACID × 2 GLYCEROL × 3 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MCRB_METBA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–433； UniProt 1–433 Author chain E； PDBConstruct 1–433； UniProt 1–433

METHYL-COENZYME M REDUCTASE SUBUNIT GAMMA

OrganismNot specified

UniProt P07964

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 SUBUNIT ALPHA × 2 （P07962） METHYL-COENZYME M REDUCTASE I BETA SUBUNIT × 2 （P07955） FACTOR 430 × 2 Coenzyme B × 2 1-THIOETHANESULFONIC ACID × 2 GLYCEROL × 3 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MCRG_METBA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–247； UniProt 1–247 Author chain F； PDBConstruct 1–247； UniProt 1–247

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	1e6y
Deposition date deposition_date	2000-08-23
Structure title title	Methyl-coenzyme M reductase from Methanosarcina barkeri
Keywords keywords	BIOLOGICAL METHANOGENESIS, NI-ENZYME, OXIDOREDUCTASE, NI ENZYME; OXIDOREDUCTASE
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.

1e6y__assembly_1__model_1

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

Download this curve (.dat)

1e6y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1e6y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.00 Å
Rg (electron density)	37.23 Å
Total Rg	37.66 Å
Atom count	19113
Residues	2485
Excluded volume	338030 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1e6y__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 (8)

Entity 1 Entity 1 polymer

Description description	METHYL-COENZYME M REDUCTASE SUBUNIT ALPHA
Molecular weight formula_weight	61951.7 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	A,D
Atom count atom_count	21340

AADIFSKFKKDMEVKFAQEFGSNKQTGGDITDKTAKFLRLGPEQDPRKVEMIKAGKEIAEKRGIAFYNPMMHSGAPLGQRAITPYTISGTDIVCEPDDLHYVNNAAMQQMWDDIRRTCIVGLDMAHETLEKRLGKEVTPETINHYLEVLNHAMPGAAVVQEMMVETHPALVDDCYVKVFTGDDALADEIDKQFLIDINKEFSEEQAAQIKASIGKTSWQAIHIPTIVSRTTDGAQTSRWAAMQIGMSFISAYAMCAGEAAVADLSFAAKHAALVSMGEMLPARRARGPNEPGGLSFGHLSDIVQTSRVSEDPAKIALEVVGAGCMLYDQIWLGSYMSGGVGFTQYATAAYTDDILDNNTYYDVDYINDKYNGAATVGKDNKVKASLEVVKDIATESTLYGIETYEKFPTALEDHFGGSQRATVLAAAAGVACSLATGNANAGLSGWYLSMYLHKEAWGRLGFFGFDLQDQCGATNVLSYQGDEGLPDELRGPNYPNYAMNVGHQGGYAGIAQAAHSGRGDAFTVNPLLKVCFADDLLPFNFAEPRREFGRGAIREFVPAGERSLVIPAK

Entity 2 Entity 2 polymer

Description description	METHYL-COENZYME M REDUCTASE I BETA SUBUNIT
Molecular weight formula_weight	45328.3 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

SDTVDIYDDRGKLLESNVDIMSLAPTRNAAIQSIIMDTKRSVAVNLAGIQGALASGKMGGKGRQILGRGLNYDIVGNADAIAENVKKLVQVDEGDDTNVIKVKGGKSLLIQSPKSRIIAGADFMSATTVGAAAVTQTIMDMFGTDPYDAPIVKSAVWGSYPQTMDLMGGQVQGILSIPQNNEGLGFSLRNIMANHVAAISNRNAMNASALSSIYEQSGIFEMGGAVGMFERHQLLGLAYQGLNANNLLYDIVKENGKDGTIGTVIESVVRRAIEAGIISVDKTAPSGYNFYKANDVPKWNACAAVGTLAATLVNCGAGRAAQNVSSTLLYFNDILEKETGLPGCDYGKVEGTAVGFSFFSHSIYGGGGPGVFNGNHVVTRHSRGFAIPCVCAAVALDAGTQMFSIESTSGLIGDVFGAIPEFREPIKAVAGVL

Entity 3 Entity 3 polymer

Description description	METHYL-COENZYME M REDUCTASE SUBUNIT GAMMA
Molecular weight formula_weight	27769.2 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

AYERQYYPGATSVAANRRKHMSGKLEKLREISDEDLTAVLGHRAPGSDYPSTHPPLAEMGEPACSTRENVAATPGAAAGDRVRYIQFADSMYNAPATPYFRSYFAAINFRGVDPGTLSGRQIVEARERDMEQCAKVQMETEITDHALAGVRGATVHGHSVRLQEDGVMFDMLDRRRLENGTIIMDKDQVAIPLDRKVDLGKPMSSEEAAKRTTIYRVDNVAFRDDAEVVEWVHRIFDQRTKFGFQPK

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 non-polymer

Description description	Coenzyme B
Molecular weight formula_weight	343.3 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	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2195

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6. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d1e6ya1
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	d1e6ya2
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	d1e6yb1
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	d1e6yb2
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	d1e6yc_
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	d1e6yd1
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	d1e6yd2
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	d1e6ye1
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	d1e6ye2
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	d1e6yf_
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	1e6yA01
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	1e6yA02
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	1e6yA03
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	1e6yB01
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	1e6yB02
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	1e6yC00
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	1e6yD01
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	1e6yD02
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	1e6yD03
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	1e6yE01
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	1e6yE02
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	1e6yF00
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	113.678 Å
Unit-cell length b length_b	153.099 Å
Unit-cell length c length_c	153.288 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1600
R_work r_work	0.1600
R_free r_free	0.1790

Methyl-coenzyme M reductase from Methanosarcina barkeri

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

METHYL-COENZYME M REDUCTASE SUBUNIT ALPHA

State in the Current Structure

Other States of the Same Protein in the Database

METHYL-COENZYME M REDUCTASE I BETA SUBUNIT

State in the Current Structure

Other States of the Same Protein in the Database

METHYL-COENZYME M REDUCTASE 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

1e6y__assembly_1__model_1

1e6y__assembly_1__model_1 | I(q)

1e6y__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

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 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 Methanosarcina barkeri

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

METHYL-COENZYME M REDUCTASE 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 BETA SUBUNIT

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 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

1e6y__assembly_1__model_1

1e6y__assembly_1__model_1 | I(q)

1e6y__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

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 water

6. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (10 domains)

CATH v4.4 (12 domains)

7. Citations (1)