1e6v

Methyl-coenzyme M reductase from Methanopyrus kandleri

Method: X-RAY DIFFRACTION

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

METHYL-COENZYME M REDUCTASE I ALPHA SUBUNIT

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 （Q49601） METHYL-COENZYME M REDUCTASE I GAMMA SUBUNIT × 2 （Q49604） FACTOR 430 × 2 Coenzyme B × 2 1-THIOETHANESULFONIC ACID × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MCRA_METKA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–553； UniProt 1–553 Author chain D； PDBConstruct 1–553； UniProt 1–553

METHYL-COENZYME M REDUCTASE I BETA SUBUNIT

OrganismNot specified

UniProt Q49601

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 ALPHA SUBUNIT × 2 （Q49605） METHYL-COENZYME M REDUCTASE I GAMMA SUBUNIT × 2 （Q49604） FACTOR 430 × 2 Coenzyme B × 2 1-THIOETHANESULFONIC ACID × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q49601
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 GAMMA SUBUNIT

OrganismNot specified

UniProt Q49604

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 ALPHA SUBUNIT × 2 （Q49605） METHYL-COENZYME M REDUCTASE I BETA SUBUNIT × 2 （Q49601） FACTOR 430 × 2 Coenzyme B × 2 1-THIOETHANESULFONIC ACID × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q49604
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–258； UniProt 1–258 Author chain F； PDBConstruct 1–258； UniProt 1–258

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	1e6v
Deposition date deposition_date	2000-08-23
Structure title title	Methyl-coenzyme M reductase from Methanopyrus kandleri
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.

1e6v__assembly_1__model_1

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

Download this curve (.dat)

1e6v__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1e6v__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.37 Å
Rg (electron density)	37.54 Å
Total Rg	37.92 Å
Atom count	19402
Residues	2458
Excluded volume	343710 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1e6v__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 (6)

Entity 1 Entity 1 polymer

Description description	METHYL-COENZYME M REDUCTASE I ALPHA SUBUNIT
Molecular weight formula_weight	61398.3 kDa
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	19402

MSSAEEKLFMKALKEKFEESPEEKYTKFYIFGGWKQSERKKEFKEWADKIVEERGVPHYNPDIGVPLGQRKLMSYQVSGTDVFVEGDDLTFVNNAAMQQMWDDIRRTVIVGMDTAHRVLERRLGKEVTPETINEYMETLNHALPGGAVVQEHMVEIHPGLTWDCYAKIITGDLELADEIDDKFLIDIEKLFPEEQAEQLIKAIGNRTYQVCRMPTIVGHVCDGATMYRWAAMQIAMSFICAYKIAAGEAAVSDFAFASKHAEVINMGEMLPARRARGENEPGGVPFGVLADCVQTMRKYPDDPAKVALEVIAAGAMLYDQIWLGSYMSGGVGFTQYATAVYPDNILDDYVYYGLEYVEDKYGIAEAEPSMDVVKDVATEVTLYGLEQYERYPAAMETHFGGSQRAAVCAAAAGCSTAFATGHAQAGLNGWYLSQILHKEGQGRLGFYGYALQDQCGAANSLSVRSDEGLPLELRGPNYPNYAMNVGHLGEYAGIVQAAHAARGDAFCVHPVIKVAFADENLVFDFTEPRKEFAKGALREFEPAGERDLIVPAE

Entity 2 Entity 2 polymer

Description description	METHYL-COENZYME M REDUCTASE I BETA SUBUNIT
Molecular weight formula_weight	48214.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

MAREAKDTVDLYDDRGNCVAEEVPIEVLSPMRNEAIQSIVNDIKRTVAVDLEGIENALQNATVGGKGMKIPGREMDVDIVDNAEAIADEIEKMIRVYQDDDTNVEPMYDGKRLLVQLPSERVKVMADPYSGTLQAGMAVVHAIIDVCEVDMWDANMVKAAVFGRYPQTIDYFGGNVASMLDVPMKQEGVGYALRNIMVNHIVAATRKNTMQAVCLAATLQQTAMFEMGDALGPFERLHLLGYAYQGLNADNMVYDIVKKHGKEGTVGTVVREVVERALEDGVIEVKEELPSFKVYKANDMDLWNAYAAAGLVAAVMVNQGAARAAQGVSATILYYNDLLEYETGLPGVDFGRAEGTAVGFSFFSHSIYGGGGPGIFHGNHIVTRHSKGFAIPPVAAAMALDAGTQMFSPEVTSKLIGDVFGEIDEFREPMKYITEAAAEEAKR

Entity 3 Entity 3 polymer

Description description	METHYL-COENZYME M REDUCTASE I GAMMA SUBUNIT
Molecular weight formula_weight	30114.8 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

MAEKAQFYYPGETDVAENRRKYMNPNYELKKLREIPDEDIVRLMGHREPGEEYPSVHPPLEEMEEPECPIRELVEPTEGAKAGDRIRYIQFTDSVYFAPIHPYIRARMYMWRYRGVDTGSLSGRQIIEVRERDLEKIAKELLETEIFDPARSGVRGATVHGHALRLDENGLMLHALRRYRLNEETGEVEYVKDQVGIELDEPIPVGAPADEDDLKERTTIYRIDGTPYREDEELLQVVQRIHELRTLAGYRPEEAEGK

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

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6. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d1e6va1
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	d1e6va2
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	d1e6vb1
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	d1e6vb2
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	d1e6vc_
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	d1e6vd1
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	d1e6vd2
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	d1e6ve1
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	d1e6ve2
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	d1e6vf_
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	1e6vA01
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	1e6vA02
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	1e6vA03
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	1e6vB01
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	1e6vB02
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	1e6vC00
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	1e6vD01
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	1e6vD02
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	1e6vD03
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	1e6vE01
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	1e6vE02
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	1e6vF00
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	80.519 Å
Unit-cell length b length_b	115.740 Å
Unit-cell length c length_c	268.510 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	2.700 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2390
R_work r_work	0.2390
R_free r_free	0.2780

Methyl-coenzyme M reductase from Methanopyrus kandleri

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

METHYL-COENZYME M REDUCTASE I ALPHA SUBUNIT

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 I GAMMA SUBUNIT

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

1e6v__assembly_1__model_1

1e6v__assembly_1__model_1 | I(q)

1e6v__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 (6)

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

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 Methanopyrus kandleri

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

METHYL-COENZYME M REDUCTASE I ALPHA 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 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 I GAMMA 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1e6v__assembly_1__model_1

1e6v__assembly_1__model_1 | I(q)

1e6v__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 (6)

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

6. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (10 domains)

CATH v4.4 (12 domains)

7. Citations (1)