- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY 3.24 Å
- Oligo State
- hetero-2-2-2-2-mer
- Ligands
- 4 x MGD: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE(Non-covalent)
- 2 x 6MO: MOLYBDENUM(VI) ION(Non-covalent)
- 4 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)(Covalent)
FES.4: 7 residues within 4Å:- Chain A: C.57, V.65, G.66, S.67, C.68, C.71, C.85
4 PLIP interactions:4 interactions with chain A,- Metal complexes: A:C.57, A:C.68, A:C.71, A:C.85
FES.13: 9 residues within 4Å:- Chain C: C.77, A.79, A.81, C.82, C.116, L.117, G.118, L.119, C.120
4 PLIP interactions:4 interactions with chain C,- Metal complexes: C:C.77, C:C.82, C:C.116, C:C.120
FES.17: 7 residues within 4Å:- Chain E: C.57, V.65, G.66, S.67, C.68, C.71, C.85
4 PLIP interactions:4 interactions with chain E,- Metal complexes: E:C.57, E:C.68, E:C.71, E:C.85
FES.26: 9 residues within 4Å:- Chain G: C.77, A.79, A.81, C.82, C.116, L.117, G.118, L.119, C.120
4 PLIP interactions:4 interactions with chain G,- Metal complexes: G:C.77, G:C.82, G:C.116, G:C.120
- 10 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
SF4.5: 8 residues within 4Å:- Chain A: H.117, D.120, C.121, C.124, A.126, C.130, T.236, A.237
4 PLIP interactions:4 interactions with chain A,- Metal complexes: A:H.117, A:C.121, A:C.124, A:C.130
SF4.6: 10 residues within 4Å:- Chain A: C.182, I.183, V.184, C.185, M.186, C.188, I.212, C.234, T.236, T.238
5 PLIP interactions:5 interactions with chain A,- Metal complexes: A:C.182, A:I.183, A:C.185, A:C.188, A:C.234
SF4.7: 11 residues within 4Å:- Chain A: F.175, C.192, T.198, L.201, C.224, V.225, S.226, C.227, G.228, A.229, C.230
5 PLIP interactions:5 interactions with chain A,- Metal complexes: A:C.192, A:C.224, A:S.226, A:C.227, A:C.230
SF4.8: 12 residues within 4Å:- Chain A: C.258, Y.260, C.261, V.263, G.264, C.265, F.267, C.293, K.295, G.296, P.428, V.429
4 PLIP interactions:4 interactions with chain A,- Metal complexes: A:C.258, A:C.261, A:C.265, A:C.293
SF4.11: 12 residues within 4Å:- Chain B: V.255, S.426, C.427, G.428, T.429, C.430, C.433, S.469, L.470, C.471, L.473, G.474
4 PLIP interactions:4 interactions with chain B,- Metal complexes: B:C.427, B:C.430, B:C.433, B:C.471
SF4.18: 8 residues within 4Å:- Chain E: H.117, D.120, C.121, C.124, A.126, C.130, T.236, A.237
4 PLIP interactions:4 interactions with chain E,- Metal complexes: E:H.117, E:C.121, E:C.124, E:C.130
SF4.19: 10 residues within 4Å:- Chain E: C.182, I.183, V.184, C.185, M.186, C.188, I.212, C.234, T.236, T.238
5 PLIP interactions:5 interactions with chain E,- Metal complexes: E:C.182, E:I.183, E:C.185, E:C.188, E:C.234
SF4.20: 11 residues within 4Å:- Chain E: F.175, C.192, T.198, L.201, C.224, V.225, S.226, C.227, G.228, A.229, C.230
5 PLIP interactions:5 interactions with chain E,- Metal complexes: E:C.192, E:C.224, E:S.226, E:C.227, E:C.230
SF4.21: 12 residues within 4Å:- Chain E: C.258, Y.260, C.261, V.263, G.264, C.265, F.267, C.293, K.295, G.296, P.428, V.429
4 PLIP interactions:4 interactions with chain E,- Metal complexes: E:C.258, E:C.261, E:C.265, E:C.293
SF4.24: 12 residues within 4Å:- Chain F: V.255, S.426, C.427, G.428, T.429, C.430, C.433, S.469, L.470, C.471, L.473, G.474
4 PLIP interactions:4 interactions with chain F,- Metal complexes: F:C.427, F:C.430, F:C.433, F:C.471
- 2 x H2S: HYDROSULFURIC ACID(Non-covalent)
- 2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)
FMN.10: 17 residues within 4Å:- Chain B: G.146, R.147, G.148, K.157, N.174, D.176, E.177, Y.254, G.257, E.258, E.259, V.292, N.293, N.294, S.297, A.472
- Ligands: NAI.12
13 PLIP interactions:13 interactions with chain B- Hydrophobic interactions: B:Y.254, B:A.472
- Hydrogen bonds: B:R.147, B:G.148, B:N.174, B:D.176, B:E.258, B:E.259, B:N.293, B:N.294, B:N.294, B:S.297
- Salt bridges: B:K.157
FMN.23: 17 residues within 4Å:- Chain F: G.146, R.147, G.148, K.157, N.174, D.176, E.177, Y.254, G.257, E.258, E.259, V.292, N.293, N.294, S.297, A.472
- Ligands: NAI.25
13 PLIP interactions:13 interactions with chain F- Hydrophobic interactions: F:Y.254, F:A.472
- Hydrogen bonds: F:R.147, F:G.148, F:N.174, F:D.176, F:E.258, F:E.259, F:N.293, F:N.294, F:N.294, F:S.297
- Salt bridges: F:K.157
- 2 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)
NAI.12: 18 residues within 4Å:- Chain A: R.79
- Chain B: A.150, F.152, K.157, T.160, E.258, E.259, L.279, P.280, V.292, K.466, S.469, L.470, C.471, A.472, G.475, F.476
- Ligands: FMN.10
8 PLIP interactions:1 interactions with chain A, 7 interactions with chain B- Hydrogen bonds: A:R.79, B:K.157, B:T.160, B:E.259, B:K.466
- Salt bridges: B:K.276
- pi-Stacking: B:F.152, B:F.152
NAI.25: 18 residues within 4Å:- Chain E: R.79
- Chain F: A.150, F.152, K.157, T.160, E.258, E.259, L.279, P.280, V.292, K.466, S.469, L.470, C.471, A.472, G.475, F.476
- Ligands: FMN.23
8 PLIP interactions:7 interactions with chain F, 1 interactions with chain E- Hydrogen bonds: F:K.157, F:T.160, F:E.259, F:K.466, E:R.79
- Salt bridges: F:K.276
- pi-Stacking: F:F.152, F:F.152
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Radon, C. et al., Cryo-EM structures reveal intricate Fe-S cluster arrangement and charging in Rhodobacter capsulatus formate dehydrogenase. Nat Commun (2020)
- Release Date
- 2020-04-22
- Peptides
- Formate dehydrogenase subunit alpha: AE
Formate dehydrogenase subunit beta: BF
Formate dehydrogenase subunit gamma: CG
NAD-dependent formate dehydrogenase subunit delta: DH - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AE
EB
BF
FC
GG
CD
DH
H
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY 3.24 Å
- Oligo State
- hetero-2-2-2-2-mer
- Ligands
- 4 x MGD: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE(Non-covalent)
- 2 x 6MO: MOLYBDENUM(VI) ION(Non-covalent)
- 4 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)(Covalent)
- 10 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 2 x H2S: HYDROSULFURIC ACID(Non-covalent)
- 2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)
- 2 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Radon, C. et al., Cryo-EM structures reveal intricate Fe-S cluster arrangement and charging in Rhodobacter capsulatus formate dehydrogenase. Nat Commun (2020)
- Release Date
- 2020-04-22
- Peptides
- Formate dehydrogenase subunit alpha: AE
Formate dehydrogenase subunit beta: BF
Formate dehydrogenase subunit gamma: CG
NAD-dependent formate dehydrogenase subunit delta: DH - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AE
EB
BF
FC
GG
CD
DH
H