- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-1-1-1-2-2-2-mer
- Ligands
- 18 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 3 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
FAD.5: 32 residues within 4Å:- Chain A: G.17, E.18, C.19, G.21, A.22, V.23, T.24, F.27, T.41, L.42, T.65, C.66, G.67, S.68, L.69, H.70, A.72, T.74, F.76, A.92, K.94, L.120, N.121, C.122, G.123, G.124, T.125, C.199, G.200, N.201, W.202, T.209
25 PLIP interactions:25 interactions with chain A- Hydrophobic interactions: A:T.125
- Hydrogen bonds: A:E.18, A:C.19, A:G.21, A:A.22, A:V.23, A:T.24, A:T.24, A:L.42, A:T.65, A:G.67, A:S.68, A:S.68, A:L.69, A:L.69, A:K.94, A:N.121, A:G.123, A:G.200, A:N.201, A:N.201, A:W.202, A:W.202, A:T.209
- pi-Stacking: A:W.202
FAD.16: 41 residues within 4Å:- Chain H: I.157, G.158, G.159, G.160, V.161, A.162, G.163, V.180, E.181, K.182, R.183, G.188, R.189, M.190, L.193, K.195, T.196, F.197, A.335, T.336, G.337, Y.338, G.360, L.361, E.364, V.410, Y.414, K.417, N.418, L.502, P.505, L.511, G.546, V.547, A.548, K.552, D.553, I.554, P.555, A.557
- Chain I: K.531
35 PLIP interactions:34 interactions with chain H, 1 interactions with chain I- Hydrophobic interactions: H:L.193, H:Y.338, H:E.364, H:Y.414, H:Y.414, H:Y.414
- Hydrogen bonds: H:G.159, H:A.162, H:E.181, H:E.181, H:K.182, H:K.182, H:G.188, H:R.189, H:M.190, H:F.197, H:F.197, H:Y.338, H:Y.338, H:Y.338, H:K.417, H:V.547, H:K.552, H:I.554, I:K.531
- Water bridges: H:G.160, H:G.160, H:V.161, H:V.161, H:G.337, H:Y.338, H:E.506, H:G.507, H:A.548
- pi-Stacking: H:F.197
FAD.26: 43 residues within 4Å:- Chain H: K.531
- Chain I: I.157, G.158, G.159, G.160, V.161, A.162, G.163, V.180, E.181, K.182, R.183, G.188, R.189, M.190, L.193, K.195, T.196, F.197, A.226, E.227, A.335, T.336, G.337, Y.338, G.360, L.361, E.364, V.410, Y.414, K.417, N.418, L.502, P.505, L.511, G.546, V.547, A.548, K.552, D.553, I.554, P.555, A.557
32 PLIP interactions:31 interactions with chain I, 1 interactions with chain H- Hydrophobic interactions: I:L.193, I:Y.338, I:L.361, I:E.364, I:Y.414, I:Y.414
- Hydrogen bonds: I:G.159, I:V.161, I:A.162, I:E.181, I:K.182, I:K.182, I:G.188, I:R.189, I:M.190, I:F.197, I:F.197, I:E.227, I:Y.338, I:Y.338, I:Y.338, I:Y.338, I:K.417, I:V.547, I:K.552, I:I.554, H:K.531
- Water bridges: I:G.160, I:G.163, I:G.337, I:A.548
- pi-Stacking: I:F.197
- 1 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 4 x 9S8: Non-cubane [4Fe-4S]-cluster(Non-covalent)
9S8.8: 15 residues within 4Å:- Chain D: F.6, G.8, C.9, I.10, C.41, C.42, A.44, P.45, C.78, G.80, C.81, P.232, F.233
- Chain F: G.129, V.130
6 PLIP interactions:6 interactions with chain D,- Metal complexes: D:C.9, D:C.41, D:C.42, D:C.78, D:C.81, D:C.81
9S8.9: 14 residues within 4Å:- Chain D: N.79, H.150, G.152, C.153, H.154, C.193, C.194, G.195, A.196, G.197, C.231, F.233, C.234
- Chain F: T.80
6 PLIP interactions:6 interactions with chain D,- Metal complexes: D:C.153, D:C.193, D:C.194, D:C.231, D:C.234, D:C.234
9S8.10: 14 residues within 4Å:- Chain E: N.79, H.150, G.152, C.153, H.154, C.193, C.194, G.195, A.196, G.197, C.231, F.233, C.234
- Chain G: T.80
6 PLIP interactions:6 interactions with chain E,- Metal complexes: E:C.153, E:C.193, E:C.194, E:C.231, E:C.234, E:C.234
9S8.11: 14 residues within 4Å:- Chain E: F.6, G.8, C.9, I.10, C.41, C.42, A.44, C.78, G.80, C.81, P.232, F.233
- Chain G: G.129, V.130
6 PLIP interactions:6 interactions with chain E,- Metal complexes: E:C.9, E:C.41, E:C.42, E:C.78, E:C.81, E:C.81
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Nomura, S. et al., Electron flow in hydrogenotrophic methanogens under nickel limitation. Nature (2025)
- Release Date
- 2025-05-14
- Peptides
- Formate dehydrogenase, beta subunit: A
Formate dehydrogenase, alpha subunit: B
Methyl viologen-reducing hydrogenase, subunit D-related protein: C
H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B: DE
H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C: FG
H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A: HI - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
EB
DC
FD
bE
BF
cG
CH
aI
A
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-1-1-1-2-2-2-mer
- Ligands
- 18 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 3 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
- 1 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 4 x 9S8: Non-cubane [4Fe-4S]-cluster(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Nomura, S. et al., Electron flow in hydrogenotrophic methanogens under nickel limitation. Nature (2025)
- Release Date
- 2025-05-14
- Peptides
- Formate dehydrogenase, beta subunit: A
Formate dehydrogenase, alpha subunit: B
Methyl viologen-reducing hydrogenase, subunit D-related protein: C
H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B: DE
H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C: FG
H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A: HI - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
EB
DC
FD
bE
BF
cG
CH
aI
A