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1gx7

Best model of the electron transfer complex between cytochrome c3 and [Fe]-hydrogenase

Dmax: 86.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PERIPLASMIC [FE] HYDROGENASE LARGE SUBUNIT

OrganismNot specified

UniProt P07598

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 27–397 Not recorded PERIPLASMIC [FE] HYDROGENASE SMALL SUBUNIT × 1 （P07603） CYTOCHROME C3 × 1 （P00131） SF4 IRON/SULFUR CLUSTER × 3 PDT 1,3-PROPANEDITHIOL × 1 FE2 FE (II) ION × 2 CYN CYANIDE ION × 2 CMO CARBON MONOXIDE × 2 HEC HEME C × 4 Experimental method not declared NMR measurement conditions：pH 5.9；296 K；Ionic strength (raw mmCIF value) 10 MM PHOSPHATE BUFFER；Pressure 1 Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1GX7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1HFE 1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS Deposited 1998-11-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 1–421（421 aa）
Not recorded ZN ZINC ION × 1 FE2 FE (II) ION × 2 CYN CYANIDE ION × 2 SF4 IRON/SULFUR CLUSTER × 3 PDT 1,3-PROPANEDITHIOL × 1 CMO CARBON MONOXIDE × 2 CYS CYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；pH 7.60
Resolution 1.60 Å R-free 0.182
1HFE 1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS Deposited 1998-11-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain M 1–421（421 aa）
Not recorded FE2 FE (II) ION × 2 CYN CYANIDE ION × 2 SF4 IRON/SULFUR CLUSTER × 3 PDT 1,3-PROPANEDITHIOL × 1 CMO CARBON MONOXIDE × 2 CYS CYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；pH 7.60
Resolution 1.60 Å R-free 0.182
1HFE 1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS Deposited 1998-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain L 1–421（421 aa）
Chain M 1–421（421 aa）
Not recorded ZN ZINC ION × 1 FE2 FE (II) ION × 4 CYN CYANIDE ION × 4 SF4 IRON/SULFUR CLUSTER × 6 PDT 1,3-PROPANEDITHIOL × 2 CMO CARBON MONOXIDE × 4 CYS CYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；pH 7.60
Resolution 1.60 Å R-free 0.182
8BJ7 Nitratidesulfovibrio vulgaris FeFe Hydrogenase C178A mutant in Hinact-like state Deposited 2022-11-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–397（396 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 VHR Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CN form) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；281.15 K；1 M Lithium chloride, 0.1 M Sodium acetate, 30 % Polyethylene glycol 4000
Resolution 1.04 Å R-free 0.167
8BJ8 Nitratidesulfovibrio vulgaris FeFe Hydrogenase C178A mutant in Htrans-like state Deposited 2022-11-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–397（396 aa）
Not recorded VHR Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CN form) × 1 SF4 IRON/SULFUR CLUSTER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；295.15 K；1 M Lithium chloride, 0.1 M Sodium acetate, 30 % Polyethylene glycol 4000
Resolution 1.01 Å R-free 0.163
8RTG Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase [FeFe]-hydrogenase in apo form Deposited 2024-01-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；1 M Lithium chloride, 0.1 M Sodium acetate, 27.5 % Polyethylene glycol 4000
Resolution 1.46 Å R-free 0.189
8RTI Nitratidesulfovibrio vulgaris [FeFe] hydrogenase in the apo form derivatized with krypton Deposited 2024-01-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded KR KRYPTON × 2 SF4 IRON/SULFUR CLUSTER × 3 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；1 M Lithium chloride, 0.1 M Sodium acetate, 35 % Polyethylene glycol 4000
Resolution 1.50 Å R-free 0.194
8RU6 Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase [FeFe]-hydrogenase variant with both subunits linked by a 4 amino acid linker peptide derived from CpI of Clostridium pasteurianum Deposited 2024-01-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–392（392 aa）
Not recorded PG4 TETRAETHYLENE GLYCOL × 4 SF4 IRON/SULFUR CLUSTER × 3 MHX Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CO form) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；0.2 M Lithium chloride, 0.1 M Sodium acetate, 25 % Polyethylene glycol 4000
Resolution 1.15 Å R-free 0.158
8RXI Nitratidesulfovibrio vulgaris [FeFe] hydrogenase in Hinact state derivatized with krypton Deposited 2024-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded KR KRYPTON × 2 SF4 IRON/SULFUR CLUSTER × 3 TOE 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL × 1 LFH dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) sulphide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；1 M Lithium chloride, 0.1 M Sodium acetate, 40 % Polyethylene glycol 4000
Resolution 1.48 Å R-free 0.181
8RXJ Nitratidesulfovibrio vulgaris [FeFe] hydrogenase C178A mutant in Hinact-like state derivatized with krypton Deposited 2024-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded KR KRYPTON × 10 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 3 CYN CYANIDE ION × 1 TOE 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；1 M Lithium chloride, 0.1 M Sodium acetate, 35 % Polyethylene glycol 4000
Resolution 1.51 Å R-free 0.186
8RYH Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase [FeFe]-hydrogenase variant with both subunits linked by a linker peptide derived from a group A1 type [FeFe]-hydrogenase of Veillonella atypica Deposited 2024-02-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–389（389 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；1 M Lithium chloride, 0.1 M Sodium acetate, 25 % Polyethylene glycol 4000
Resolution 1.77 Å R-free 0.246
9GBU Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase variant with both subunits linked by a 13 amino acid linker peptide derived from a group A1 type [FeFe]-hydrogenase of Solobacterium moorei Deposited 2024-07-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–389（389 aa）
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；50% MPD, 0.1 HEPES pH 7.6
Resolution 1.78 Å R-free 0.242
9GBU Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase variant with both subunits linked by a 13 amino acid linker peptide derived from a group A1 type [FeFe]-hydrogenase of Solobacterium moorei Deposited 2024-07-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–389（389 aa）
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；50% MPD, 0.1 HEPES pH 7.6
Resolution 1.78 Å R-free 0.242
9GNK Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase variant with both subunits linked by a 13 amino acid linker peptide derived from CpI of Clostridium pasteurianum Deposited 2024-09-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–390（390 aa）
Not recorded CMO CARBON MONOXIDE × 2 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 2 SF4 IRON/SULFUR CLUSTER × 6 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 PG4 TETRAETHYLENE GLYCOL × 6 PEG DI(HYDROXYETHYL)ETHER × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5, 20 % Polyethylene glycol 1500
Resolution 1.05 Å R-free 0.185
9GZ0 FeFe Hydrogenase from Desulfovibrio desulfuricans labelled with cyanophenylalanine - oxidised state Deposited 2024-10-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–397（396 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SF4 IRON/SULFUR CLUSTER × 3 4WW bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)[mu-propane-1,3-bis(thiolate)-1kappa~2~S~1~,S~3~:2kappa~2~S~1~,S~3~] diiron(2+) × 1 CL CHLORIDE ION × 3 LI LITHIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；296 K；0.9 M LiSO4 100 mM Na Acetate 24-30% PEG 6000
Resolution 1.02 Å R-free 0.166
9GZ4 FeFe Hydrogenase from Desulfovibrio desulfuricans labelled with cyanophenylalanine - reduced state Deposited 2024-10-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–397（396 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SF4 IRON/SULFUR CLUSTER × 3 4WW bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)[mu-propane-1,3-bis(thiolate)-1kappa~2~S~1~,S~3~:2kappa~2~S~1~,S~3~] diiron(2+) × 1 CL CHLORIDE ION × 3 LI LITHIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；296 K；0.9 M LiSO4 100 mM Na Acetate 24-30% Peg 6000
Resolution 0.96 Å R-free 0.152
9GZL Apo FeFe Hydrogenase from Desulfovibrio desulfuricans labelled with cyanophenylalanine Deposited 2024-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–397（396 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SF4 IRON/SULFUR CLUSTER × 3 CL CHLORIDE ION × 7 LI LITHIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；296 K；0.9 M LiSO4 100 mM Na Acetate 24-30% Peg 6000
Resolution 1.02 Å R-free 0.153
9HPX [FeFe]-hydrogenase from D. desulfuricans with synthetic active site containing only one cyanide ligand. Deposited 2024-12-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–397（396 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 A1IW2 6,6,7,7-tetrakis($l^{3}-oxidanylidynemethyl)-1$l^{3},5$l^{3}-dithia-3-aza-6$l^{5},7$l^{4}-diferrabicyclo[3.1.1]heptane-6-carbonitrile × 1 CL CHLORIDE ION × 10 LI LITHIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；296 K；0.9 M LiCl 0.1 M Sodium Acetate 26-32% PEG 6000
Resolution 0.96 Å R-free 0.144
9QD6 High resolution structure of the artificially maturated [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough Deposited 2025-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 3 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；30% (w/v) PEG 4000, 1M LiCl, 0.1M sodium acetate
Resolution 1.18 Å R-free 0.169
9QDC Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase crystallized in the sodium formate buffer at pH 4.6 Deposited 2025-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；35% (w/v) PEG 4000, 1M LiCl, 0.1M sodium formate pH 4.6
Resolution 1.49 Å R-free 0.181
9QDD Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase crystallized in the sodium acetate buffer at pH 5.3 Deposited 2025-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；293 K；30% (w/v) PEG 4000, 1M LiCl, 0.1M sodium acetate pH 5.3
Resolution 1.20 Å R-free 0.220
9QDG Nitratidesulfovibrio vulgaris [FeFe] hydrogenase crystallized in the sodium propionate buffer at pH 5.0 Deposited 2025-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；30% (w/v) PEG 4000, 1M LiCl, 0.1M sodium propionate pH 5.0
Resolution 1.02 Å R-free 0.207
9QIS CO-bound [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris Deposited 2025-03-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 CMO CARBON MONOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；37% (w/v) PEG 4000, 1M LiCl, 0.1M sodium acetate
Resolution 1.49 Å R-free 0.176
9R9Q [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 5.04 Deposited 2025-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.62 Å R-free 0.197
9R9R [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 5.21 Deposited 2025-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.58 Å R-free 0.202
9R9S [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 5.45 Deposited 2025-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.71 Å R-free 0.174
9R9T [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 5.81 Deposited 2025-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.08 Å R-free 0.242
9R9U [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 6.62 Deposited 2025-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–397（397 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.31 Å R-free 0.162
9R9V [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 7.00 Deposited 2025-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–395（394 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.25 Å R-free 0.153

26 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PHFL_DESVH
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–371； UniProt 27–397

PERIPLASMIC [FE] HYDROGENASE SMALL SUBUNIT

OrganismNot specified

UniProt P07603

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain D； UniProt 36–123 Not recorded PERIPLASMIC [FE] HYDROGENASE LARGE SUBUNIT × 1 （P07598） CYTOCHROME C3 × 1 （P00131） SF4 IRON/SULFUR CLUSTER × 3 PDT 1,3-PROPANEDITHIOL × 1 FE2 FE (II) ION × 2 CYN CYANIDE ION × 2 CMO CARBON MONOXIDE × 2 HEC HEME C × 4 Experimental method not declared NMR measurement conditions：pH 5.9；296 K；Ionic strength (raw mmCIF value) 10 MM PHOSPHATE BUFFER；Pressure 1 Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1GX7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1HFE 1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS Deposited 1998-11-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain S 1–123（123 aa）
Not recorded ZN ZINC ION × 1 FE2 FE (II) ION × 2 CYN CYANIDE ION × 2 SF4 IRON/SULFUR CLUSTER × 3 PDT 1,3-PROPANEDITHIOL × 1 CMO CARBON MONOXIDE × 2 CYS CYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；pH 7.60
Resolution 1.60 Å R-free 0.182
1HFE 1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS Deposited 1998-11-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain T 1–123（123 aa）
Not recorded FE2 FE (II) ION × 2 CYN CYANIDE ION × 2 SF4 IRON/SULFUR CLUSTER × 3 PDT 1,3-PROPANEDITHIOL × 1 CMO CARBON MONOXIDE × 2 CYS CYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；pH 7.60
Resolution 1.60 Å R-free 0.182
1HFE 1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS Deposited 1998-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain S 1–123（123 aa）
Chain T 1–123（123 aa）
Not recorded ZN ZINC ION × 1 FE2 FE (II) ION × 4 CYN CYANIDE ION × 4 SF4 IRON/SULFUR CLUSTER × 6 PDT 1,3-PROPANEDITHIOL × 2 CMO CARBON MONOXIDE × 4 CYS CYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；pH 7.60
Resolution 1.60 Å R-free 0.182
8BJ7 Nitratidesulfovibrio vulgaris FeFe Hydrogenase C178A mutant in Hinact-like state Deposited 2022-11-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 VHR Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CN form) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；281.15 K；1 M Lithium chloride, 0.1 M Sodium acetate, 30 % Polyethylene glycol 4000
Resolution 1.04 Å R-free 0.167
8BJ8 Nitratidesulfovibrio vulgaris FeFe Hydrogenase C178A mutant in Htrans-like state Deposited 2022-11-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded VHR Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CN form) × 1 SF4 IRON/SULFUR CLUSTER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；295.15 K；1 M Lithium chloride, 0.1 M Sodium acetate, 30 % Polyethylene glycol 4000
Resolution 1.01 Å R-free 0.163
8RTG Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase [FeFe]-hydrogenase in apo form Deposited 2024-01-26 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；1 M Lithium chloride, 0.1 M Sodium acetate, 27.5 % Polyethylene glycol 4000
Resolution 1.46 Å R-free 0.189
8RTI Nitratidesulfovibrio vulgaris [FeFe] hydrogenase in the apo form derivatized with krypton Deposited 2024-01-26 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded KR KRYPTON × 2 SF4 IRON/SULFUR CLUSTER × 3 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；1 M Lithium chloride, 0.1 M Sodium acetate, 35 % Polyethylene glycol 4000
Resolution 1.50 Å R-free 0.194
8RU6 Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase [FeFe]-hydrogenase variant with both subunits linked by a 4 amino acid linker peptide derived from CpI of Clostridium pasteurianum Deposited 2024-01-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 39–123（85 aa）
Not recorded PG4 TETRAETHYLENE GLYCOL × 4 SF4 IRON/SULFUR CLUSTER × 3 MHX Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CO form) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；0.2 M Lithium chloride, 0.1 M Sodium acetate, 25 % Polyethylene glycol 4000
Resolution 1.15 Å R-free 0.158
8RXI Nitratidesulfovibrio vulgaris [FeFe] hydrogenase in Hinact state derivatized with krypton Deposited 2024-02-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded KR KRYPTON × 2 SF4 IRON/SULFUR CLUSTER × 3 TOE 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL × 1 LFH dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) sulphide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；1 M Lithium chloride, 0.1 M Sodium acetate, 40 % Polyethylene glycol 4000
Resolution 1.48 Å R-free 0.181
8RXJ Nitratidesulfovibrio vulgaris [FeFe] hydrogenase C178A mutant in Hinact-like state derivatized with krypton Deposited 2024-02-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded KR KRYPTON × 10 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 3 CYN CYANIDE ION × 1 TOE 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；1 M Lithium chloride, 0.1 M Sodium acetate, 35 % Polyethylene glycol 4000
Resolution 1.51 Å R-free 0.186
8RYH Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase [FeFe]-hydrogenase variant with both subunits linked by a linker peptide derived from a group A1 type [FeFe]-hydrogenase of Veillonella atypica Deposited 2024-02-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 46–123（78 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；1 M Lithium chloride, 0.1 M Sodium acetate, 25 % Polyethylene glycol 4000
Resolution 1.77 Å R-free 0.246
9GBU Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase variant with both subunits linked by a 13 amino acid linker peptide derived from a group A1 type [FeFe]-hydrogenase of Solobacterium moorei Deposited 2024-07-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 46–123（78 aa）
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；50% MPD, 0.1 HEPES pH 7.6
Resolution 1.78 Å R-free 0.242
9GBU Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase variant with both subunits linked by a 13 amino acid linker peptide derived from a group A1 type [FeFe]-hydrogenase of Solobacterium moorei Deposited 2024-07-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 46–123（78 aa）
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；50% MPD, 0.1 HEPES pH 7.6
Resolution 1.78 Å R-free 0.242
9GNK Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase variant with both subunits linked by a 13 amino acid linker peptide derived from CpI of Clostridium pasteurianum Deposited 2024-09-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 45–123（79 aa）
Not recorded CMO CARBON MONOXIDE × 2 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 2 SF4 IRON/SULFUR CLUSTER × 6 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 PG4 TETRAETHYLENE GLYCOL × 6 PEG DI(HYDROXYETHYL)ETHER × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5, 20 % Polyethylene glycol 1500
Resolution 1.05 Å R-free 0.185
9GZ0 FeFe Hydrogenase from Desulfovibrio desulfuricans labelled with cyanophenylalanine - oxidised state Deposited 2024-10-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 4WW bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)[mu-propane-1,3-bis(thiolate)-1kappa~2~S~1~,S~3~:2kappa~2~S~1~,S~3~] diiron(2+) × 1 CL CHLORIDE ION × 3 LI LITHIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；296 K；0.9 M LiSO4 100 mM Na Acetate 24-30% PEG 6000
Resolution 1.02 Å R-free 0.166
9GZ4 FeFe Hydrogenase from Desulfovibrio desulfuricans labelled with cyanophenylalanine - reduced state Deposited 2024-10-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 4WW bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)[mu-propane-1,3-bis(thiolate)-1kappa~2~S~1~,S~3~:2kappa~2~S~1~,S~3~] diiron(2+) × 1 CL CHLORIDE ION × 3 LI LITHIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；296 K；0.9 M LiSO4 100 mM Na Acetate 24-30% Peg 6000
Resolution 0.96 Å R-free 0.152
9GZL Apo FeFe Hydrogenase from Desulfovibrio desulfuricans labelled with cyanophenylalanine Deposited 2024-10-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 CL CHLORIDE ION × 7 LI LITHIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；296 K；0.9 M LiSO4 100 mM Na Acetate 24-30% Peg 6000
Resolution 1.02 Å R-free 0.153
9HPX [FeFe]-hydrogenase from D. desulfuricans with synthetic active site containing only one cyanide ligand. Deposited 2024-12-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 A1IW2 6,6,7,7-tetrakis($l^{3}-oxidanylidynemethyl)-1$l^{3},5$l^{3}-dithia-3-aza-6$l^{5},7$l^{4}-diferrabicyclo[3.1.1]heptane-6-carbonitrile × 1 CL CHLORIDE ION × 10 LI LITHIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；296 K；0.9 M LiCl 0.1 M Sodium Acetate 26-32% PEG 6000
Resolution 0.96 Å R-free 0.144
9QD6 High resolution structure of the artificially maturated [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough Deposited 2025-03-06 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 3 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；30% (w/v) PEG 4000, 1M LiCl, 0.1M sodium acetate
Resolution 1.18 Å R-free 0.169
9QDC Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase crystallized in the sodium formate buffer at pH 4.6 Deposited 2025-03-06 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；35% (w/v) PEG 4000, 1M LiCl, 0.1M sodium formate pH 4.6
Resolution 1.49 Å R-free 0.181
9QDD Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase crystallized in the sodium acetate buffer at pH 5.3 Deposited 2025-03-06 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；293 K；30% (w/v) PEG 4000, 1M LiCl, 0.1M sodium acetate pH 5.3
Resolution 1.20 Å R-free 0.220
9QDG Nitratidesulfovibrio vulgaris [FeFe] hydrogenase crystallized in the sodium propionate buffer at pH 5.0 Deposited 2025-03-06 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 SF4 IRON/SULFUR CLUSTER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；30% (w/v) PEG 4000, 1M LiCl, 0.1M sodium propionate pH 5.0
Resolution 1.02 Å R-free 0.207
9QIS CO-bound [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris Deposited 2025-03-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 402 dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) × 1 CMO CARBON MONOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；37% (w/v) PEG 4000, 1M LiCl, 0.1M sodium acetate
Resolution 1.49 Å R-free 0.176
9R9Q [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 5.04 Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.62 Å R-free 0.197
9R9R [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 5.21 Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.58 Å R-free 0.202
9R9S [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 5.45 Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.71 Å R-free 0.174
9R9T [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 5.81 Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.08 Å R-free 0.242
9R9U [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 6.62 Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.31 Å R-free 0.162
9R9V [FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 7.00 Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–123（88 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.25 Å R-free 0.153

26 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PHFS_DESVH
Isoform —
PDB entities 2
Chains and sequence ranges Author chain D； PDBConstruct 1–88； UniProt 36–123

CYTOCHROME C3

OrganismNot specified

UniProt P00131

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain E； UniProt 23–129 Not recorded PERIPLASMIC [FE] HYDROGENASE LARGE SUBUNIT × 1 （P07598） PERIPLASMIC [FE] HYDROGENASE SMALL SUBUNIT × 1 （P07603） SF4 IRON/SULFUR CLUSTER × 3 PDT 1,3-PROPANEDITHIOL × 1 FE2 FE (II) ION × 2 CYN CYANIDE ION × 2 CMO CARBON MONOXIDE × 2 HEC HEME C × 4 Experimental method not declared NMR measurement conditions：pH 5.9；296 K；Ionic strength (raw mmCIF value) 10 MM PHOSPHATE BUFFER；Pressure 1 Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1GX7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A2I SOLUTION STRUCTURE OF DESULFOVIBRIO VULGARIS (HILDENBOROUGH) FERROCYTOCHROME C3, NMR, 20 STRUCTURES Deposited 1998-01-05 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–129（107 aa）
Not recorded HEC HEME C × 4 SOLUTION NMR
NMR measurement conditions pH 8.5；303 K
Resolution not provided
1MDV KEY ROLE OF PHENYLALANINE 20 IN CYTOCHROME C3: STRUCTURE, STABILITY AND FUNCTION STUDIES Deposited 1998-09-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–129（107 aa）
Mutation：F20L HEM PROTOPORPHYRIN IX CONTAINING FE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；pH 7.6
Resolution 2.30 Å R-free 0.296
1MDV KEY ROLE OF PHENYLALANINE 20 IN CYTOCHROME C3: STRUCTURE, STABILITY AND FUNCTION STUDIES Deposited 1998-09-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 23–129（107 aa）
Mutation：F20L HEM PROTOPORPHYRIN IX CONTAINING FE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；pH 7.6
Resolution 2.30 Å R-free 0.296
1MDV KEY ROLE OF PHENYLALANINE 20 IN CYTOCHROME C3: STRUCTURE, STABILITY AND FUNCTION STUDIES Deposited 1998-09-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 23–129（107 aa）
Chain B 23–129（107 aa）
Mutation：F20L Mutation：F20L HEM PROTOPORPHYRIN IX CONTAINING FE × 32 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；pH 7.6
Resolution 2.30 Å R-free 0.296
2BPN SOLUTION STRUCTURE OF DESULFOVIBRIO VULGARIS (HILDENBOROUGH) FERRICYTOCHROME C3, NMR, 20 STRUCTURES Deposited 2005-04-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–129（107 aa） Fragment：CYTOCHROME C3, RESIDUES 23-129
Not recorded HEC HEME C × 4 SOLUTION NMR
NMR measurement conditions pH 7.1；303 K
NMR sample composition 92% WATER/8% D2O AND 100% D2O
Resolution not provided
2CTH CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH Deposited 1997-06-18 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–129（107 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；PROTEIN WAS CRYSTALLIZED FROM 75% (V/V) ETHANOL AND 0.05 M SODIUM ACETATE (PH 5.5)
Resolution 1.67 Å R-free 0.190
2CTH CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH Deposited 1997-06-18 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 23–129（107 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；PROTEIN WAS CRYSTALLIZED FROM 75% (V/V) ETHANOL AND 0.05 M SODIUM ACETATE (PH 5.5)
Resolution 1.67 Å R-free 0.190
2CYM EFFECTS OF AMINO ACID SUBSTITUTION ON THREE-DIMENSIONAL STRUCTURE: AN X-RAY ANALYSIS OF CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH AT 2 ANGSTROMS RESOLUTION Deposited 1993-09-29 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–129（107 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å

5 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CYC3_DESVH
Isoform —
PDB entities 3
Chains and sequence ranges Author chain E； PDBConstruct 1–107； UniProt 23–129

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1gx7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1gx7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1gx7
Deposition date deposition_date2002-03-28
Structure title titleBest model of the electron transfer complex between cytochrome c3 and [Fe]-hydrogenase
Keywords keywords;OXIDOREDUCTASE, ELECTRON TRANSFER COMPLEX, HYDROGENASE, MULTIHEME CYTOCHROME, SOFT DOCKING, OXIDOREDUCTASE ELECTRON TRANSPORT, 4FE-4S, IRON-SULFUR ;; OXIDOREDUCTASE
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.87 Å
Radius of gyration Rg (electron density) rg_electron24.50 Å
Forward intensity I(0) i073235100.00
Molecular weight molecular_weight65778.0 kDa
Excluded volume excluded_volume81408 ų
Envelope volume envelope_volume89524 ų
Hydration-shell volume shell_volume30208 ų
Envelope diameter envelope_diameter91.9 Å
Shell Rg shell_rg32.23 Å
Envelope Rg envelope_rg25.06 Å
Shape Rg shape_rg24.61 Å
Total Rg total_rg24.92 Å
Total atoms total_atoms5509
Residues n_residues566
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax86.8 Å
Rg (real space) rg_real25.88 Å
Rg uncertainty (real space) rg_real_error0.29 Å
I(0) (real space) i0_real7.3200e+07
I(0) uncertainty (real space) i0_real_error8.2770e+05
Rg (reciprocal space) rg_reciprocal24.91 Å
I(0) (reciprocal space) i0_reciprocal73230000.0000
Solution quality estimate total_estimate0.6551
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks0
Primary peak position r_peak_primary— Å
Skewness Skewness skewness0.545
Kurtosis Kurtosis kurtosis-0.038
Angular range angular_range— – 0.3200 Å−1
Current regularization parameter α current_alpha4.5790
Highest regularization parameter α highest_alpha27340000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.785; Stabil: 0.894; Sysdev: 0.000; Positv: 1.000; Valcen: 0.907; Smooth: 0.614
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

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8. Citations (1)

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9. Files and Curves (10)