1e3d

[NiFe] Hydrogenase from Desulfovibrio desulfuricans ATCC 27774

Method: X-RAY DIFFRACTION

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

[NiFe] hydrogenase small 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 2	[NiFe] hydrogenase large subunit × 1 （Q9L868） FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1 BIS-(MU-2-OXO),[(MU-3--SULFIDO)-BIS(MU-2--SULFIDO)-TRIS(CYS-S)-TRI-IRON] (AQUA)(GLU-O)IRON(II) × 1 HYDROSULFURIC ACID × 2 (MU-SULPHIDO)-BIS(MU-CYS,S)-[TRICARBONYLIRON-DI-(CYS,S)NICKEL(II)](FE-NI) × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	[NiFe] hydrogenase large subunit × 1 （Q9L868） FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1 BIS-(MU-2-OXO),[(MU-3--SULFIDO)-BIS(MU-2--SULFIDO)-TRIS(CYS-S)-TRI-IRON] (AQUA)(GLU-O)IRON(II) × 1 HYDROSULFURIC ACID × 2 (MU-SULPHIDO)-BIS(MU-CYS,S)-[TRICARBONYLIRON-DI-(CYS,S)NICKEL(II)](FE-NI) × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9L869_DESDE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–266； UniProt 1–266 Author chain C； PDBConstruct 1–266； UniProt 1–266

[NiFe] hydrogenase large subunit

OrganismNot specified

UniProt Q9L868

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	[NiFe] hydrogenase small subunit × 1 （Q9L869） FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1 BIS-(MU-2-OXO),[(MU-3--SULFIDO)-BIS(MU-2--SULFIDO)-TRIS(CYS-S)-TRI-IRON] (AQUA)(GLU-O)IRON(II) × 1 HYDROSULFURIC ACID × 2 (MU-SULPHIDO)-BIS(MU-CYS,S)-[TRICARBONYLIRON-DI-(CYS,S)NICKEL(II)](FE-NI) × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	[NiFe] hydrogenase small subunit × 1 （Q9L869） FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1 BIS-(MU-2-OXO),[(MU-3--SULFIDO)-BIS(MU-2--SULFIDO)-TRIS(CYS-S)-TRI-IRON] (AQUA)(GLU-O)IRON(II) × 1 HYDROSULFURIC ACID × 2 (MU-SULPHIDO)-BIS(MU-CYS,S)-[TRICARBONYLIRON-DI-(CYS,S)NICKEL(II)](FE-NI) × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9L868_DESDE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–542； UniProt 2–543 Author chain D； PDBConstruct 1–542； UniProt 2–543

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	1e3d
Deposition date deposition_date	2000-06-14
Structure title title	[NiFe] Hydrogenase from Desulfovibrio desulfuricans ATCC 27774
Keywords keywords	HYDROGENASE, MOLECULAR MODELLING, ELECTRON TRANSFER; HYDROGENASE
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.

1e3d__assembly_1__model_1

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

Download this curve (.dat)

1e3d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1e3d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.67 Å
Rg (electron density)	24.69 Å
Total Rg	25.45 Å
Atom count	12211
Residues	799
Excluded volume	110390 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1e3d__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1e3d__assembly_2__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	[NiFe] hydrogenase small subunit
Molecular weight formula_weight	28682.6 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	25867

ALTGSRPSVVYLHAAECTGCSEALLRTYQPFIDTLILDTISLDYHETIMAAAGEAAEEALQAAVNGPDGFICLVEGAIPTGMDNKYGYIAGHTMYDICKNILPKAKAVVSIGTCACYGGIQAAKPNPTAAKGINDCYADLGVKAINVPGCPPNPLNMVGTLVAFLKGQKIELDEVGRPVMFFGQSVHDLCERRKHFDAGEFAPSFNSEEARKGWCLYDVGCKGPETYNNCPKVLFNETNWPVAAGHPCIGCSEPNFWDDMTPFYQN

Entity 2 Entity 2 polymer

Description description	[NiFe] hydrogenase large subunit
Molecular weight formula_weight	60009.9 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

SQVTKTPRSNYTGPIVVDPLTRIEGHLRIEVEVEGGVIKEARSCATLFRGIETILKGRDPRDAQHFTQRTCGVCTYTHALASTRCLEDAINKPIPANATYIRNLVLGNQFMHDHLVHFYHLHALDFVDVTSALLADPAKAAKLANSISPRKATTEEFAAVQAKLKTFVASGQLGPFTNAYFLGGHEGYYMDPEANLVCTAHYLQALRAQVEVAKGMAVFGAKNPHTQFTVAGGVTCYEALTPERIKQFRELYVKARAFIEEVYIPDLLLVASYYKDWGKIGGTNNFMAFGEFPAPGGERDLNSRWYKPGVIYDRKVGSVQPFDPSKIEEHVRHSWYEGKARAPFEGETNPHFTFMGDTDKYSWNKAPRYDGHAVETGPLAQMLVAYGHNHKTIKPTIDAVLGKLNLGPEALFSTLGRTAARGIQTLVIAQQMENWLNEYENNIVKDKQIVEDYAVPTSARGVGFADVSRGGLSHWMTIEDGKIDNFQLVVPTTWNLGPRDDKGVPSAAEAALVGTPVADPKRPVEILRTIHSFDPCIACSTH

Entity 3 Entity 3 non-polymer

Description description	FE3-S4 CLUSTER
Molecular weight formula_weight	295.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	BIS-(MU-2-OXO),[(MU-3--SULFIDO)-BIS(MU-2--SULFIDO)-TRIS(CYS-S)-TRI-IRON] (AQUA)(GLU-O)IRON(II)
Molecular weight formula_weight	367.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 non-polymer

Description description	(MU-SULPHIDO)-BIS(MU-CYS,S)-[TRICARBONYLIRON-DI-(CYS,S)NICKEL(II)](FE-NI)
Molecular weight formula_weight	230.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1399

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1e3da_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.19 — HydA/Nqo6-like
Superfamily Superfamily superfamily	e.19.1 — HydA/Nqo6-like
Family Family family	e.19.1.1 — Nickel-iron hydrogenase, small subunit

Domain ID domain_id	d1e3db_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.18 — HydB/Nqo4-like
Superfamily Superfamily superfamily	e.18.1 — HydB/Nqo4-like
Family Family family	e.18.1.1 — Nickel-iron hydrogenase, large subunit

Domain ID domain_id	d1e3dc_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.19 — HydA/Nqo6-like
Superfamily Superfamily superfamily	e.19.1 — HydA/Nqo6-like
Family Family family	e.19.1.1 — Nickel-iron hydrogenase, small subunit

Domain ID domain_id	d1e3dd_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.18 — HydB/Nqo4-like
Superfamily Superfamily superfamily	e.18.1 — HydB/Nqo4-like
Family Family family	e.18.1.1 — Nickel-iron hydrogenase, large subunit

CATH v4.4 (6 domains)

Domain ID domain_id	1e3dA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	700 — NADH:ubiquinone oxidoreductase-like, 20kDa subunit

Domain ID domain_id	1e3dA02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	480 — Cytochrome-c3 Hydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome-c3 hydrogenase, C-terminal domain

Domain ID domain_id	1e3dB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	645 — Cytochrome-c3 Hydrogenase; chain B
Homologous superfamily homologous superfamily	10 — Cytochrome-c3 Hydrogenase, chain B

Domain ID domain_id	1e3dC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	700 — NADH:ubiquinone oxidoreductase-like, 20kDa subunit

Domain ID domain_id	1e3dC02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	480 — Cytochrome-c3 Hydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome-c3 hydrogenase, C-terminal domain

Domain ID domain_id	1e3dD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	645 — Cytochrome-c3 Hydrogenase; chain B
Homologous superfamily homologous superfamily	10 — Cytochrome-c3 Hydrogenase, chain B

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Unit-cell length a length_a	64.090 Å
Unit-cell length b length_b	169.980 Å
Unit-cell length c length_c	72.620 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.80 °
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	1.800 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.1671
R_work r_work	—
R_free r_free	0.2231

[NiFe] Hydrogenase from Desulfovibrio desulfuricans ATCC 27774

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

[NiFe] hydrogenase small subunit

State in the Current Structure

Other States of the Same Protein in the Database

[NiFe] hydrogenase large 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

1e3d__assembly_1__model_1

1e3d__assembly_1__model_1 | I(q)

1e3d__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 (9)

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 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)

[NiFe] Hydrogenase from Desulfovibrio desulfuricans ATCC 27774

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

[NiFe] hydrogenase small 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

[NiFe] hydrogenase large 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

1e3d__assembly_1__model_1

1e3d__assembly_1__model_1 | I(q)

1e3d__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 (9)

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 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)