6x5k

Crystal structure of CODH/ACS with carbon monoxide bound to the A-cluster

Method: X-RAY DIFFRACTION

▼

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

Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha × 2 （P27988） IRON/SULFUR CLUSTER × 5 FE(4)-NI(1)-S(4) CLUSTER × 2 TRIETHYLENE GLYCOL × 1 NICKEL (II) ION × 4 CARBON MONOXIDE × 2 MAGNESIUM ION × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha × 2 （P27988） IRON/SULFUR CLUSTER × 5 FE(4)-NI(1)-S(4) CLUSTER × 2 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE × 1 NICKEL (II) ION × 4 CARBON MONOXIDE × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DCMB_MOOTH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–674； UniProt 1–674 Author chain B； PDBConstruct 1–674； UniProt 1–674 Author chain C； PDBConstruct 1–674； UniProt 1–674 Author chain D； PDBConstruct 1–674； UniProt 1–674

Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha

OrganismNot specified

UniProt P27988

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta × 2 （P27989） IRON/SULFUR CLUSTER × 5 FE(4)-NI(1)-S(4) CLUSTER × 2 TRIETHYLENE GLYCOL × 1 NICKEL (II) ION × 4 CARBON MONOXIDE × 2 MAGNESIUM ION × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta × 2 （P27989） IRON/SULFUR CLUSTER × 5 FE(4)-NI(1)-S(4) CLUSTER × 2 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE × 1 NICKEL (II) ION × 4 CARBON MONOXIDE × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DCMA_MOOTH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain M； PDBConstruct 1–729； UniProt 1–729 Author chain N； PDBConstruct 1–729； UniProt 1–729 Author chain O； PDBConstruct 1–729； UniProt 1–729 Author chain P； PDBConstruct 1–729； UniProt 1–729

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6x5k
Deposition date deposition_date	2020-05-26
Structure title title	Crystal structure of CODH/ACS with carbon monoxide bound to the A-cluster
Keywords keywords	CODH, ACS, carbon monoxide dehydrogenase, acetyl-CoA synthase, OXIDOREDUCTASE, OXIDOREDUCTASE-TRANSFERASE complex; OXIDOREDUCTASE/TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

6x5k__assembly_1__model_1

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

Download this curve (.dat)

6x5k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6x5k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	51.32 Å
Rg (electron density)	52.08 Å
Total Rg	51.77 Å
Atom count	21745
Residues	2800
Excluded volume	389110 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6x5k__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6x5k__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta
Molecular weight formula_weight	73006.9 kDa
EC 编号 ec_number	1.2.7.4
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	44026

MPRFRDLSHNCRPSEAPRVMEPKNRDRTVDPAVLEMLVKSKDDKVITAFDRFVAQQPQCKIGYEGICCRFCMAGPCRIKATDGPGSRGICGASAWTIVARNVGLMILTGAAAHCEHGNHIAHALVEMAEGKAPDYSVKDEAKLKEVCRRVGIEVEGKSVLELAQEVGEKALEDFRRLKGEGEATWLMTTINEGRKEKFRTHNVVPFGIHASISELVNQAHMGMDNDPVNLVFSAIRVALADYTGEHIATDFSDILFGTPQPVVSEANMGVLDPDQVNFVLHGHNPLLSEIIVQAAREMEGEAKAAGAKGINLVGICCTGNEVLMRQGIPLVTSFASQELAICTGAIDAMCVDVQCIMPSISAVAECYHTRIITTADNAKIPGAYHIDYQTATAIESAKTAIRMAIEAFKERKESNRPVYIPQIKNRVVAGWSLEALTKLLATQNAQNPIRVLNQAILDGELAGVALICGCNNLKGFQDNSHLTVMKELLKNNVFVVATGCSAQAAGKLGLLDPANVETYCGDGLKGFLKRLGEGANIEIGLPPVFHMGSCVDNSRAVDLLMAMANDLGVDTPKVPFVASAPEAMSGKAAAIGTWWVSLGVPTHVGTMPPVEGSDLIYSILTQIASDVYGGYFIFEMDPQVAARKILDALEYRTWKLGVHKEVAERYETKLCQGY

Entity 2 Entity 2 polymer

Description description	Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
Molecular weight formula_weight	81816.9 kDa
EC 编号 ec_number	2.3.1.169
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N,O,P

MTDFDKIFEGAIPEGKEPVALFREVYHGAITATSYAEILLNQAIRTYGPDHPVGYPDTAYYLPVIRCFSGEEVKKLGDLPPILNRKRAQVSPVLNFENARLAGEATWYAAEIIEALRYLKYKPDEPLLPPPWTGFIGDPVVRRFGIKMVDWTIPGEAIILGRAKDSKALAKIVKELMGMGFMLFICDEAVEQLLEENVKLGIDYIAYPLGNFTQIVHAANYALRAGMMFGGVTPGAREEQRDYQRRRIRAFVLYLGEHDMVKTAAAFGAIFTGFPVITDQPLPEDKQIPDWFFSVEDYDKIVQIAMETRGIKLTKIKLDLPINFGPAFEGESIRKGDMYVEMGGNRTPAFELVRTVSESEITDGKIEVIGPDIDQIPEGSKLPLGILVDIYGRKMQADFEGVLERRIHDFINYGEGLWHTGQRNINWLRVSKDAVAKGFRFKNYGEILVAKMKEEFPAIVDRVQVTIFTDEAKVKEYMEVAREKYKERDDRMRGLTDETVDTFYSCVLCQSFAPNHVCIVTPERVGLCGAVSWLDAKASYEINHAGPNQPIPKEGEIDPIKGIWKSVNDYLYTASNRNLEQVCLYTLMENPMTSCGCFEAIMAILPECNGIMITTRDHAGMTPSGMTFSTLAGMIGGGTQTPGFMGIGRTYIVSKKFISADGGIARIVWMPKSLKDFLHDEFVRRSVEEGLGEDFIDKIADETIGTTVDEILPYLEEKGHPALTMDPIM

Entity 3 Entity 3 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 4 Entity 4 non-polymer

Description description	FE(4)-NI(1)-S(4) CLUSTER
Molecular weight formula_weight	410.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
Molecular weight formula_weight	178.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 8 Entity 8 non-polymer

Description description	CARBON MONOXIDE
Molecular weight formula_weight	28.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 9 Entity 9 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	468

▼

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d6x5ka_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.26 — Prismane protein-like
Superfamily Superfamily superfamily	e.26.1 — Prismane protein-like
Family Family family	e.26.1.2 — Carbon monoxide dehydrogenase

Domain ID domain_id	d6x5kb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.26 — Prismane protein-like
Superfamily Superfamily superfamily	e.26.1 — Prismane protein-like
Family Family family	e.26.1.2 — Carbon monoxide dehydrogenase

Domain ID domain_id	d6x5kc_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.26 — Prismane protein-like
Superfamily Superfamily superfamily	e.26.1 — Prismane protein-like
Family Family family	e.26.1.2 — Carbon monoxide dehydrogenase

Domain ID domain_id	d6x5kd_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.26 — Prismane protein-like
Superfamily Superfamily superfamily	e.26.1 — Prismane protein-like
Family Family family	e.26.1.2 — Carbon monoxide dehydrogenase

Domain ID domain_id	d6x5km_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.26 — Prismane protein-like
Superfamily Superfamily superfamily	e.26.1 — Prismane protein-like
Family Family family	e.26.1.3 — Acetyl-CoA synthase

Domain ID domain_id	d6x5kn_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.26 — Prismane protein-like
Superfamily Superfamily superfamily	e.26.1 — Prismane protein-like
Family Family family	e.26.1.3 — Acetyl-CoA synthase

Domain ID domain_id	d6x5ko_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.26 — Prismane protein-like
Superfamily Superfamily superfamily	e.26.1 — Prismane protein-like
Family Family family	e.26.1.3 — Acetyl-CoA synthase

Domain ID domain_id	d6x5kp_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.26 — Prismane protein-like
Superfamily Superfamily superfamily	e.26.1 — Prismane protein-like
Family Family family	e.26.1.3 — Acetyl-CoA synthase

▶

Unit-cell length a length_a	99.729 Å
Unit-cell length b length_b	137.383 Å
Unit-cell length c length_c	141.867 Å
Unit-cell angle α angle_alpha	101.82 °
Unit-cell angle β angle_beta	109.08 °
Unit-cell angle γ angle_gamma	103.66 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	2.470 Å
Low-resolution limit resolution_low	49.630 Å
R factor r_factor	0.2049
R_work r_work	0.2034
R_free r_free	0.2336

Crystal structure of CODH/ACS with carbon monoxide bound to the A-cluster

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

Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha

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

6x5k__assembly_1__model_1

6x5k__assembly_1__model_1 | I(q)

6x5k__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

7. Citations (1)

Crystal structure of CODH/ACS with carbon monoxide bound to the A-cluster

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

Carbon monoxide dehydrogenase/acetyl-CoA synthase 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

Carbon monoxide dehydrogenase/acetyl-CoA synthase 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6x5k__assembly_1__model_1

6x5k__assembly_1__model_1 | I(q)

6x5k__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

7. Citations (1)