SMTL ID : 7bke.1

Formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex from Methanospirillum hungatei (heterodisulfide reductase core and mobile arm in conformational state 2, composite structure)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-1-1-1-mer

Ligands

18 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 11 residues within 4Å: Chain A: L.401, C.402, S.405, R.406, C.416, S.417, R.418, C.420, C.421, D.446, R.448 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.402, A:C.416, A:C.420, A:C.421 SF4.3: 12 residues within 4Å: Chain A: V.245, G.260, C.261, N.262, G.263, C.264, G.265, C.267, Y.301, C.318, K.321, I.324 6 PLIP interactions: 6 interactions with chain A, Salt bridges: A:D.266 pi-Cation interactions: A:Y.301 Metal complexes: A:C.261, A:C.264, A:C.267, A:C.318 SF4.4: 13 residues within 4Å: Chain A: C.271, P.272, V.273, A.288, I.289, C.308, V.309, K.310, C.311, G.312, L.313, C.314, L.326 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.271, A:C.308, A:C.311, A:C.314 SF4.5: 12 residues within 4Å: Chain B: C.54, P.55, Y.62, I.64, C.88, T.89, T.90, C.91, Y.92, S.93, C.94, T.105 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.54, B:C.88, B:C.91, B:C.94 SF4.6: 12 residues within 4Å: Chain B: C.44, Y.45, Q.46, C.47, G.48, T.49, C.50, R.65, M.68, C.98, P.99, P.104 5 PLIP interactions: 5 interactions with chain B, pi-Cation interactions: B:Y.45 Metal complexes: B:C.44, B:C.47, B:C.50, B:C.98 SF4.9: 11 residues within 4Å: Chain D: L.401, C.402, S.405, R.406, C.416, S.417, R.418, C.420, C.421, D.446, R.448 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.402, D:C.416, D:C.420, D:C.421 SF4.11: 9 residues within 4Å: Chain D: C.14, C.16, I.20, Q.46, Y.47, C.49, C.74, F.83, R.103 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.14, D:C.16, D:C.49, D:C.74 SF4.12: 12 residues within 4Å: Chain D: L.609, C.610, Y.612, A.614, L.615, C.633, K.634, G.635, C.636, G.637, C.639, M.650 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.610, D:C.633, D:C.636, D:C.639 SF4.13: 10 residues within 4Å: Chain D: C.600, A.601, G.602, C.603, G.604, C.606, F.642, C.643, A.647, I.648 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.600, D:C.603, D:C.606, D:C.643 SF4.14: 12 residues within 4Å: Chain D: V.245, G.260, C.261, N.262, G.263, C.264, G.265, C.267, Y.301, C.318, K.321, I.324 6 PLIP interactions: 6 interactions with chain D, Salt bridges: D:D.266 pi-Cation interactions: D:Y.301 Metal complexes: D:C.261, D:C.264, D:C.267, D:C.318 SF4.15: 13 residues within 4Å: Chain D: C.271, P.272, V.273, A.288, I.289, C.308, V.309, K.310, C.311, G.312, L.313, C.314, L.326 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.271, D:C.308, D:C.311, D:C.314 SF4.17: 7 residues within 4Å: Chain D: P.644 Chain F: V.300, C.306, C.308, C.311, S.312, H.337 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.306, F:C.308, F:C.311, F:H.337 SF4.18: 13 residues within 4Å: Chain F: C.293, I.294, K.295, C.296, Y.297, A.298, C.299, F.330, H.331, C.352, P.353, I.356, N.358 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.293, F:C.296, F:C.299, F:C.352 SF4.19: 13 residues within 4Å: Chain F: C.303, P.304, I.305, R.334, V.338, C.342, I.343, N.344, C.345, G.346, C.348, A.359, M.362 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.303, F:C.342, F:C.345, F:C.348 SF4.20: 11 residues within 4Å: Chain F: K.101, G.102, C.103, C.129, G.131, N.189, C.190, C.193, M.195, K.196, N.344 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.103, F:C.129, F:C.190, F:C.193 SF4.22: 12 residues within 4Å: Chain G: C.54, P.55, Y.62, I.64, C.88, T.89, T.90, C.91, Y.92, S.93, C.94, T.105 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.54, G:C.88, G:C.91, G:C.94 SF4.23: 12 residues within 4Å: Chain G: C.44, Y.45, Q.46, C.47, G.48, T.49, C.50, R.65, M.68, C.98, P.99, P.104 5 PLIP interactions: 5 interactions with chain G, pi-Cation interactions: G:Y.45 Metal complexes: G:C.44, G:C.47, G:C.50, G:C.98 SF4.26: 10 residues within 4Å: Chain I: C.15, Y.17, C.18, G.21, C.22, L.49, C.50, K.52, G.53, L.184 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.15, I:C.18, I:C.22, I:C.50

3 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.2: 36 residues within 4Å: Chain A: V.153, G.154, G.155, G.156, V.157, A.158, I.176, E.177, R.178, T.179, G.184, R.185, L.189, K.191, T.192, F.193, A.343, T.344, G.345, Y.346, A.368, L.369, E.372, F.419, Y.423, K.426, N.514, L.520, G.555, V.556, K.561, D.562, I.563, P.564, T.566 Chain D: K.540 23 PLIP interactions: 22 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:L.189, A:Y.346, A:A.368, A:L.369, A:F.419, A:Y.423, A:Y.423 Hydrogen bonds: A:G.155, A:V.157, A:A.158, A:R.178, A:R.178, A:R.185, A:M.186, A:F.193, A:F.193, A:Y.346, A:K.426, A:V.556, A:K.561, A:I.563, D:K.540 pi-Stacking: A:F.193 FAD.10: 36 residues within 4Å: Chain A: K.540 Chain D: V.153, G.154, G.155, G.156, V.157, A.158, I.176, E.177, R.178, T.179, G.184, R.185, L.189, K.191, T.192, F.193, A.343, T.344, G.345, Y.346, A.368, L.369, E.372, F.419, Y.423, K.426, N.514, L.520, G.555, V.556, K.561, D.562, I.563, P.564, T.566 23 PLIP interactions: 22 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:L.189, D:Y.346, D:A.368, D:L.369, D:F.419, D:Y.423, D:Y.423 Hydrogen bonds: D:G.155, D:V.157, D:A.158, D:R.178, D:R.178, D:R.185, D:M.186, D:F.193, D:F.193, D:Y.346, D:K.426, D:V.556, D:K.561, D:I.563, A:K.540 pi-Stacking: D:F.193 FAD.21: 29 residues within 4Å: Chain F: G.21, E.22, C.23, G.24, G.25, A.26, V.27, T.28, L.31, A.45, I.46, T.69, A.70, G.71, S.72, L.73, H.74, G.76, T.99, K.101, V.127, N.128, C.129, G.130, G.131, G.206, N.207, W.208, T.219 28 PLIP interactions: 28 interactions with chain F Hydrogen bonds: F:E.22, F:C.23, F:G.24, F:G.25, F:A.26, F:V.27, F:T.28, F:T.28, F:I.46, F:T.69, F:T.69, F:G.71, F:S.72, F:S.72, F:L.73, F:G.76, F:G.76, F:K.101, F:N.128, F:G.130, F:N.207, F:N.207, F:N.207, F:W.208, F:W.208, F:T.219 pi-Stacking: F:W.208 pi-Cation interactions: F:H.74

4 x 9S8: Non-cubane [4Fe-4S]-cluster(Non-covalent)

9S8.7: 10 residues within 4Å: Chain B: G.138 Chain C: G.9, C.10, I.11, C.42, C.43, C.79, G.81, C.82, F.237 6 PLIP interactions: 6 interactions with chain C, Metal complexes: C:C.10, C:C.42, C:C.43, C:C.79, C:C.82, C:C.82 9S8.8: 8 residues within 4Å: Chain C: H.154, G.156, C.157, C.197, C.198, C.235, F.237, C.238 7 PLIP interactions: 7 interactions with chain C, pi-Cation interactions: C:H.158 Metal complexes: C:C.157, C:C.197, C:C.198, C:C.235, C:C.238, C:C.238 9S8.24: 10 residues within 4Å: Chain G: G.138 Chain H: G.9, C.10, I.11, C.42, C.43, C.79, G.81, C.82, F.237 6 PLIP interactions: 6 interactions with chain H, Metal complexes: H:C.10, H:C.42, H:C.43, H:C.79, H:C.82, H:C.82 9S8.25: 8 residues within 4Å: Chain H: H.154, G.156, C.157, C.197, C.198, C.235, F.237, C.238 7 PLIP interactions: 7 interactions with chain H, pi-Cation interactions: H:H.158 Metal complexes: H:C.157, H:C.197, H:C.198, H:C.235, H:C.238, H:C.238

1 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.16: 9 residues within 4Å: Chain E: C.14, W.16, C.43, T.44, G.67, C.68, C.73, H.74, N.79 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.14, E:C.43, E:C.68, E:C.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watanabe, T. et al., Three-megadalton complex of methanogenic electron-bifurcating and CO 2 -fixing enzymes. Science (2021)

Release Date

2021-09-29

Peptides

CoB--CoM heterodisulfide reductase iron-sulfur subunit A: AD
CoB--CoM heterodisulfide reductase subunit C: BG
CoB--CoM heterodisulfide reductase subunit B: CH
F420-non-reducing hydrogenase subunit D: E
Formate dehydrogenase, beta subunit (F420): F
Formate dehydrogenase: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
a

B
C

G
c

C
B

H
b

E
F

F
E

I
D

CoB--CoM heterodisulfide reductase iron-sulfur subunit A

CoB--CoM heterodisulfide reductase subunit C

CoB--CoM heterodisulfide reductase subunit B

F420-non-reducing hydrogenase subunit D

Formate dehydrogenase, beta subunit (F420)

Formate dehydrogenase

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