8cm5

W-formate dehydrogenase C872A from Desulfovibrio vulgaris

Method: X-RAY DIFFRACTION

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

Formate dehydrogenase, alpha subunit, selenocysteine-containing

Desulfovibrio vulgaris str. Hildenborough

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Formate dehydrogenase, beta subunit, putative × 1 （Q72EJ0） DI(HYDROXYETHYL)ETHER × 1 HYDROSULFURIC ACID × 1 TUNGSTEN ION × 1 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 2 IRON/SULFUR CLUSTER × 4 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Formate dehydrogenase, beta subunit, putative × 1 （Q72EJ0） DI(HYDROXYETHYL)ETHER × 2 HYDROSULFURIC ACID × 1 TUNGSTEN ION × 1 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 2 IRON/SULFUR CLUSTER × 4 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Formate dehydrogenase, beta subunit, putative × 1 （Q72EJ0） DI(HYDROXYETHYL)ETHER × 2 HYDROSULFURIC ACID × 1 TUNGSTEN ION × 1 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 2 IRON/SULFUR CLUSTER × 4 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Formate dehydrogenase, beta subunit, putative × 1 （Q72EJ0） DI(HYDROXYETHYL)ETHER × 1 HYDROSULFURIC ACID × 1 TUNGSTEN ION × 1 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 2 IRON/SULFUR CLUSTER × 4 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q72EJ1_DESVH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1005； UniProt 1–1005 Author chain C； PDBConstruct 1–1005； UniProt 1–1005 Author chain K； PDBConstruct 1–1005； UniProt 1–1005 Author chain R； PDBConstruct 1–1005； UniProt 1–1005

Formate dehydrogenase, beta subunit, putative

Desulfovibrio vulgaris str. Hildenborough

UniProt Q72EJ0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Formate dehydrogenase, alpha subunit, selenocysteine-containing × 1 （Q72EJ1） DI(HYDROXYETHYL)ETHER × 1 HYDROSULFURIC ACID × 1 TUNGSTEN ION × 1 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 2 IRON/SULFUR CLUSTER × 4 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Formate dehydrogenase, alpha subunit, selenocysteine-containing × 1 （Q72EJ1） DI(HYDROXYETHYL)ETHER × 2 HYDROSULFURIC ACID × 1 TUNGSTEN ION × 1 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 2 IRON/SULFUR CLUSTER × 4 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Formate dehydrogenase, alpha subunit, selenocysteine-containing × 1 （Q72EJ1） DI(HYDROXYETHYL)ETHER × 2 HYDROSULFURIC ACID × 1 TUNGSTEN ION × 1 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 2 IRON/SULFUR CLUSTER × 4 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Formate dehydrogenase, alpha subunit, selenocysteine-containing × 1 （Q72EJ1） DI(HYDROXYETHYL)ETHER × 1 HYDROSULFURIC ACID × 1 TUNGSTEN ION × 1 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 2 IRON/SULFUR CLUSTER × 4 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q72EJ0_DESVH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–215； UniProt 1–215 Author chain D； PDBConstruct 1–215； UniProt 1–215 Author chain L； PDBConstruct 1–215； UniProt 1–215 Author chain S； PDBConstruct 1–215； UniProt 1–215

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	8cm5
Deposition date deposition_date	2023-02-17
Structure title title	W-formate dehydrogenase C872A from Desulfovibrio vulgaris
Keywords keywords	Formate, CO2, Molybdenum and Tungsten enzymes, DMSO reductase family, ELECTRON TRANSPORT, OXIDOREDUCTASE; 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.

8cm5__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8cm5__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8cm5__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	30.12 Å
Rg (electron density)	29.50 Å
Total Rg	30.15 Å
Atom count	9426
Residues	1187
Excluded volume	167270 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8cm5__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8cm5__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`8cm5__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`8cm5__assembly_4__model_1`	dimeric （2）	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 (9)

Entity 1 Entity 1 polymer

Description description	Formate dehydrogenase, alpha subunit, selenocysteine-containing
Molecular weight formula_weight	112405.0 kDa
Mutation mutation	C872A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,K,R
Atom count atom_count	38677

MTVTRRHFLKLSAGAAVAGAFTGLGLSLAPTVARAELQKLQWAKQTTSICCYCAVGCGLIVHTAKDGQGRAVNVEGDPDHPINEGSLCPKGASIFQLGENDQRGTQPLYRAPFSDTWKPVTWDFALTEIAKRIKKTRDASFTEKNAAGDLVNRTEAIASFGSAAMDNEECWAYGNILRSLGLVYIEHQARIUHSPTVPALAESFGRGAMTNHWNDLANSDCILIMGSNAAENHPIAFKWVLRAKDKGATLIHVDPRFTRTSARCDVYAPIRSGADIPFLGGLIKYILDNKLYFTDYVREYTNASLIVGEKFSFKDGLFSGYDAANKKYDKSMWAFELDANGVPKRDPALKHPRCVINLLKKHYERYNLDKVAAITGTSKEQLQQVYKAYAATGKPDKAGTIMYAMGWTQHSVGVQNIRAMAMIQLLLGNIGVAGGGVNALRGESNVQGSTDQGLLAHIWPGYNPVPNSKAATLELYNAATPQSKDPMSVNWWQNRPKYVASYLKALYPDEEPAAAYDYLPRIDAGRKLTDYFWLNIFEKMDKGEFKGLFAWGMNPACGGANANKNRKAMGKLEWLVNVNLFENETSSFWKGPGMNPAEIGTEVFFLPCCVSIEKEGSVANSGRWMQWRYRGPKPYAETKPDGDIMLDMFKKVRELYAKEGGAYPAPIAKLNIADWEEHNEFSPTKVAKLMNGYFLKDTEVGGKQFKKGQQVPSFAFLTADGSTCSGNWLHAGSFTDAGNLMARRDKTQTPEQARIGLFPNWSFCWPVNRRILYNRASVDKTGKPWNPAKAVIEWKDGKWVGDVVDGGGDPGTKHPFIMQTHGFGALYGPGREEGPFPEHYEPLECPVSKNPFSKQLHNPVAFQIEGEKKAVADPRYPFIGTTYRVTEHWQTGLMTRRCAWLVEAEPQIFCEISKELAKLRGIGNGDTVKVSSLRGALEAVAIVTERIRPFKIEGVDVHMVGLPWHYGWMVPKNGGDTANLLTPSAGDPNTGIPETKAFMVDVRKVWSHPQFEK

Source Source

Source organism organism	Desulfovibrio vulgaris str. Hildenborough
NCBI taxonomy ID ncbi_taxonomy_id	882
Host organism host_organism	Desulfovibrio vulgaris str. Hildenborough

Entity 2 Entity 2 polymer

Description description	Formate dehydrogenase, beta subunit, putative
Molecular weight formula_weight	23989.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,L,S

MGKMFFVDLSRCTACRGCQIACKQWKNLPAEETRNTGSHQNPPDLSYVTLKTVRFTEKSRKGPGIDWLFFPEQCRHCVEPPCKGQADVDLEGAVVKDETTGAVLFTELTAKVDGESVRSACPYDIPRIDPVTKRLSKCDMCNDRVQNGLLPACVKTCPTGTMNFGDEQEMLALAEKRLAEVKKTYPGAVLGDPNDVRVVYLFTRDPKDFYEHAVA

Source Source

Source organism organism	Desulfovibrio vulgaris str. Hildenborough
NCBI taxonomy ID ncbi_taxonomy_id	882
Host organism host_organism	Desulfovibrio vulgaris str. Hildenborough

Entity 3 Entity 3 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	HYDROSULFURIC ACID
Molecular weight formula_weight	34.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	TUNGSTEN ION
Molecular weight formula_weight	183.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
Molecular weight formula_weight	740.6 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 7 Entity 7 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 8 Entity 8 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	963

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Unit-cell length a length_a	73.440 Å
Unit-cell length b length_b	261.055 Å
Unit-cell length c length_c	126.209 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.58 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	48.831 Å
R factor r_factor	—
R_work r_work	0.1840
R_free r_free	0.2396

W-formate dehydrogenase C872A from Desulfovibrio vulgaris

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

Formate dehydrogenase, alpha subunit, selenocysteine-containing

State in the Current Structure

Other States of the Same Protein in the Database

Formate dehydrogenase, beta subunit, putative

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

8cm5__assembly_4__model_1

8cm5__assembly_4__model_1 | I(q)

8cm5__assembly_4__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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 water

7. Citations (1)

W-formate dehydrogenase C872A from Desulfovibrio vulgaris

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

Formate dehydrogenase, alpha subunit, selenocysteine-containing

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Formate dehydrogenase, beta subunit, putative

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

8cm5__assembly_4__model_1

8cm5__assembly_4__model_1 | I(q)

8cm5__assembly_4__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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 water

7. Citations (1)