Electron bifurcating hydrogenase - HydABC from A. woodii
Resolution: 4.7 Å
EM Method: Single-particle
Fitted PDBs: 7q4v
Q-score: 0.211
Katsyv A, Kumar A, Saura P, Poverlein MC, Freibert SA, T Stripp S, Jain S, Gamiz-Hernandez AP, Kaila VRI, Muller V, Schuller JM
J Am Chem Soc (2023) 145 pp. 5696-5709 [ Pubmed: 36811855 DOI: doi:10.1021/jacs.2c11683 ]
- Iron/sulfur cluster (351 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- Iron hydrogenase hydc (16 kDa, Protein from Acetobacterium woodii DSM 1030)
- Homodimer complex of hydabc trimer (300 MDa, Complex from Acetobacterium woodii DSM 1030)
- Iron hydrogenase hyda1 (63 kDa, Protein from Acetobacterium woodii DSM 1030)
- Iron hydrogenase hydb (64 kDa, Protein from Acetobacterium woodii DSM 1030)
- Flavin mononucleotide (456 Da, Ligand)
- Zinc ion (65 Da, Ligand)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8a5e
Q-score: 0.409
Katsyv A, Kumar A, Saura P, Poverlein MC, Freibert SA, T Stripp S, Jain S, Gamiz-Hernandez AP, Kaila VRI, Muller V, Schuller JM
J Am Chem Soc (2023) 145 pp. 5696-5709 [ Pubmed: 36811855 DOI: doi:10.1021/jacs.2c11683 ]
- Iron/sulfur cluster (351 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Iron hydrogenase hydc (16 kDa, Protein from Acetobacterium woodii DSM 1030)
- Zinc ion (65 Da, Ligand)
- Iron hydrogenase hyda1 (63 kDa, Protein from Acetobacterium woodii DSM 1030)
- Iron hydrogenase hydb (64 kDa, Protein from Acetobacterium woodii DSM 1030)
- Flavin mononucleotide (456 Da, Ligand)
- Electron bifurcating fe-fe hydrogenase hydabc complex from thermoanaerobacter kivui (348 kDa, Complex from Thermoanaerobacter kivui)
- 1,4-dihydronicotinamide adenine dinucleotide (665 Da, Ligand)
- 2 iron/2 sulfur/5 carbonyl/2 water inorganic cluster (355 Da, Ligand)
Resolution: 3.78 Å
EM Method: Single-particle
Fitted PDBs: 7q4w
Q-score: 0.253
Katsyv A, Kumar A, Saura P, Poverlein MC, Freibert SA, T Stripp S, Jain S, Gamiz-Hernandez AP, Kaila VRI, Muller V, Schuller JM
J Am Chem Soc (2023) 145 pp. 5696-5709 [ DOI: doi:10.1021/jacs.2c11683 Pubmed: 36811855 ]
- Flavin mononucleotide (456 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Homodimer complex of hydabc trimer (350 MDa, Complex from Acetobacterium woodii DSM 1030)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Iron hydrogenase hydb (50 kDa, Protein from Acetobacterium woodii DSM 1030)
- Iron hydrogenase hydc (16 kDa, Protein from Acetobacterium woodii DSM 1030)
- Zinc ion (65 Da, Ligand)
- Iron hydrogenase hyda1 (63 kDa, Protein from Acetobacterium woodii DSM 1030)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8a6t
Q-score: 0.46
Katsyv A, Kumar A, Saura P, Poverlein MC, Freibert SA, T Stripp S, Jain S, Gamiz-Hernandez AP, Kaila VRI, Muller V, Schuller JM
J Am Chem Soc (2023) 145 pp. 5696-5709 [ Pubmed: 36811855 DOI: doi:10.1021/jacs.2c11683 ]
- Iron/sulfur cluster (351 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Electron bifurcating hydrogenase subunit hydb (68 kDa, Protein from Thermoanaerobacter kivui)
- Electron bifurcating hydrogenase subunit hydc (18 kDa, Protein from Thermoanaerobacter kivui)
- Zinc ion (65 Da, Ligand)
- Nadp nicotinamide-adenine-dinucleotide phosphate (743 Da, Ligand)
- Flavin mononucleotide (456 Da, Ligand)
- Electron bifurcating fe-fe hydrogenase hydabc complex from thermoanaerobacter kivui (348 kDa, Complex from Thermoanaerobacter kivui)
- Electron bifurcating hydrogenase subunit hyda1 (63 kDa, Protein from Thermoanaerobacter kivui)
- 2 iron/2 sulfur/5 carbonyl/2 water inorganic cluster (355 Da, Ligand)
Resolution: 3.49 Å
EM Method: Single-particle
Fitted PDBs: 8bew
Q-score: 0.411
Katsyv A, Kumar A, Saura P, Poverlein MC, Freibert SA, T Stripp S, Jain S, Gamiz-Hernandez AP, Kaila VRI, Muller V, Schuller JM
J Am Chem Soc (2023) 145 pp. 5696-5709 [ DOI: doi:10.1021/jacs.2c11683 Pubmed: 36811855 ]
- Flavin mononucleotide (456 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Electron bifurcating hydrogenase subunit hydb (68 kDa, Protein from Thermoanaerobacter kivui)
- Electron bifurcating hydrogenase subunit hyda1 (63 kDa, Protein from Thermoanaerobacter kivui)
- Zinc ion (65 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Dimer of the trimeric hydabc complex (Complex from Thermoanaerobacter kivui)
- Electron bifurcating hydrogenase subunit hydc (18 kDa, Protein from Thermoanaerobacter kivui)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8d4t
Q-score: 0.545
Di Trani JM, Moe A, Riepl D, Saura P, Kaila VRI, Brzezinski P, Rubinstein JL
PNAS (2022) 119 pp. e2205228119-e2205228119 [ DOI: doi:10.1073/pnas.2205228119 Pubmed: 35858451 ]
- Cytochrome c oxidase subunit 5b, mitochondrial (10 kDa, Protein from cattle)
- Cytochrome c oxidase subunit 7a1, mitochondrial (6 kDa, Protein from cattle)
- Cytochrome c oxidase subunit 6a2, mitochondrial (8 kDa, Protein from cattle)
- Cytochrome c oxidase subunit 1 (56 kDa, Protein from cattle)
- Sodium ion (22 Da, Ligand)
- (1s)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(stearoyloxy)methyl]ethyl (5e,8e,11e,14e)-icosa-5,8,11,14-tetraenoate (768 Da, Ligand)
- Cytochrome c oxidase subunit 4 isoform 1, mitochondrial (16 kDa, Protein from cattle)
- Zinc ion (65 Da, Ligand)
- Cytochrome c oxidase subunit 8a, mitochondrial (4 kDa, Protein from cattle)
- Cytochrome c oxidase subunit 2 (26 kDa, Protein from cattle)
- Cytochrome c oxidase subunit 3 (29 kDa, Protein from cattle)
- Cytochrome c oxidase subunit 6b1 (9 kDa, Protein from cattle)
- Magnesium ion (24 Da, Ligand)
- Heme-a (852 Da, Ligand)
- Cytochrome c oxidase subunit 7c, mitochondrial (5 kDa, Protein from cattle)
- (3beta,14beta,17beta,25r)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en (544 Da, Ligand)
- Cytochrome c oxidase subunit 7b, mitochondrial (5 kDa, Protein from cattle)
- Cytochrome c oxidase (Complex from Bos taurus)
- Copper (ii) ion (63 Da, Ligand)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Cytochrome c oxidase subunit 5a, mitochondrial (11 kDa, Protein from cattle)
- Cytochrome c oxidase subunit 6c (8 kDa, Protein from cattle)
Structure of the NDH-1MS complex from Thermosynechococcus elongatus
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 6tjv
Q-score: 0.529
Schuller JM, Saura P, Thiemann J, Schuller SK, Gamiz-Hernandez AP, Kurisu G, Nowaczyk MM, Kaila VRI
Nat Commun (2020) 11 pp. 494-494 [ Pubmed: 31980611 DOI: doi:10.1038/s41467-020-14347-4 ]
- Nad(p)h-quinone oxidoreductase subunit h (45 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Nad(p)h-quinone oxidoreductase subunit i (22 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Nad(p)h-quinone oxidoreductase subunit 4l (11 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Nadh dehydrogenase subunit 4 (53 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Chlorophyll a (893 Da, Ligand)
- Nad(p)h-quinone oxidoreductase subunit l (8 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Beta-carotene (536 Da, Ligand)
- Ndh-1ms (Complex from Thermosynechococcus elongatus BP-1)
- Nad(p)h-quinone oxidoreductase subunit k (25 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Zinc ion (65 Da, Ligand)
- Nadh dehydrogenase subunit 6 (21 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Tlr0906 protein (51 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Nad(p)h-quinone oxidoreductase subunit 3 (15 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Water (18 Da, Ligand)
- Nad(p)h-quinone oxidoreductase subunit 1 (40 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Tlr0636 protein (12 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Nad(p)h-quinone oxidoreductase subunit j (19 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Nadh dehydrogenase subunit 5 (66 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- (1s)-2-{[{[(2r)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate (751 Da, Ligand)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Nad(p)h-quinone oxidoreductase subunit m (12 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Nad(p)h-quinone oxidoreductase subunit n (16 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Nad(p)h-quinone oxidoreductase subunit 2 (55 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Nad(p)h-quinone oxidoreductase subunit o (7 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Iron/sulfur cluster (351 Da, Ligand)
- Tll0220 protein (15 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))