SMTL ID : 7bkd.1

Formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex from Methanospirillum hungatei (heterodislfide reductase core and mobile arm in conformational state 1, 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, C.416, S.417, R.418, F.419, 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: 11 residues within 4Å: Chain A: C.14, C.16, I.20, Y.47, M.48, C.49, A.73, C.74, H.79, R.103 Chain D: N.262 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.14, A:C.16, A:C.49, A:C.74 SF4.4: 11 residues within 4Å: Chain A: C.610, Y.612, L.615, C.633, K.634, G.635, C.636, G.637, T.638, C.639, M.650 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.610, A:C.633, A:C.636, A:C.639 SF4.5: 9 residues within 4Å: Chain A: C.600, A.601, G.602, C.603, G.604, C.606, M.626, C.643, I.648 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.600, A:C.603, A:C.606, A:C.643 SF4.6: 11 residues within 4Å: Chain A: V.245, C.261, N.262, G.263, C.264, G.265, C.267, Y.301, C.318, K.321, A.323 5 PLIP interactions: 5 interactions with chain A, pi-Cation interactions: A:Y.301 Metal complexes: A:C.261, A:C.264, A:C.267, A:C.318 SF4.7: 14 residues within 4Å: Chain A: C.271, P.272, V.273, A.288, I.289, V.303, 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 SF4.8: 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 SF4.9: 11 residues within 4Å: Chain B: C.44, 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 SF4.12: 11 residues within 4Å: Chain D: L.401, C.402, S.405, C.416, S.417, R.418, F.419, 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 SF4.14: 13 residues within 4Å: Chain D: V.245, C.261, N.262, G.263, C.264, G.265, D.266, C.267, Y.301, C.318, K.321, A.323, I.324 5 PLIP interactions: 5 interactions with chain D, pi-Cation interactions: D:Y.301 Metal complexes: D:C.261, D:C.264, D:C.267, D:C.318 SF4.15: 14 residues within 4Å: Chain D: C.271, P.272, V.273, A.288, I.289, V.303, 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 SF4.16: 12 residues within 4Å: Chain E: 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 E, Metal complexes: E:C.54, E:C.88, E:C.91, E:C.94 SF4.17: 11 residues within 4Å: Chain E: C.44, 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 E, pi-Cation interactions: E:Y.45 Metal complexes: E:C.44, E:C.47, E:C.50, E:C.98 SF4.21: 7 residues within 4Å: Chain A: P.644 Chain H: V.300, C.306, C.308, C.311, S.312, H.337 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.306, H:C.308, H:C.311, H:H.337 SF4.22: 11 residues within 4Å: Chain H: C.293, I.294, K.295, C.296, Y.297, C.299, F.330, H.331, C.352, I.356, N.358 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.293, H:C.296, H:C.299, H:C.352 SF4.23: 12 residues within 4Å: Chain H: C.303, 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 H, Metal complexes: H:C.303, H:C.342, H:C.345, H:C.348 SF4.24: 12 residues within 4Å: Chain H: K.101, G.102, C.103, C.129, G.131, S.132, N.189, C.190, C.193, M.195, K.196, N.344 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.103, H:C.129, H:C.190, H:C.193 SF4.26: 10 residues within 4Å: Chain I: C.15, Y.17, C.18, G.21, C.22, L.49, C.50, G.53, P.183, 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: 35 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, I.182, G.184, R.185, L.189, K.191, T.192, F.193, A.343, T.344, G.345, Y.346, A.368, E.372, F.419, Y.423, K.426, L.520, G.555, V.556, K.561, D.562, I.563, P.564, T.566 Chain D: K.540 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:L.189, A:Y.346, A:A.368, A:E.372, 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:I.182, 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 pi-Stacking: A:F.193 FAD.13: 34 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, I.182, G.184, R.185, L.189, K.191, T.192, F.193, A.343, T.344, G.345, Y.346, A.368, E.372, F.419, Y.423, K.426, L.520, G.555, V.556, K.561, D.562, I.563, T.566 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:L.189, D:Y.346, D:A.368, D:E.372, D:F.419, D:Y.423 Hydrogen bonds: D:G.155, D:V.157, D:A.158, D:R.178, D:R.178, D:I.182, 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 pi-Stacking: D:F.193 pi-Cation interactions: D:R.178 FAD.25: 29 residues within 4Å: Chain H: G.21, E.22, C.23, G.24, G.25, A.26, V.27, T.28, L.31, A.45, I.46, T.69, G.71, S.72, L.73, H.74, G.76, T.99, K.101, V.127, N.128, C.129, G.130, G.131, S.132, G.206, N.207, W.208, T.219 26 PLIP interactions: 26 interactions with chain H Hydrophobic interactions: H:V.127 Hydrogen bonds: H:E.22, H:C.23, H:G.25, H:A.26, H:V.27, H:T.28, H:T.28, H:T.28, H:I.46, H:T.69, H:G.71, H:S.72, H:S.72, H:L.73, H:L.73, H:G.76, H:K.101, H:N.128, H:G.130, H:N.207, H:N.207, H:W.208, H:W.208, H:T.219 pi-Cation interactions: H:H.74

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

9S8.10: 10 residues within 4Å: Chain B: V.139 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 9S8.11: 9 residues within 4Å: Chain C: H.154, G.156, C.157, H.158, 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 9S8.18: 10 residues within 4Å: Chain E: V.139 Chain F: 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 F, Metal complexes: F:C.10, F:C.42, F:C.43, F:C.79, F:C.82, F:C.82 9S8.19: 9 residues within 4Å: Chain F: H.154, G.156, C.157, H.158, C.197, C.198, C.235, F.237, C.238 7 PLIP interactions: 7 interactions with chain F, pi-Cation interactions: F:H.158 Metal complexes: F:C.157, F:C.197, F:C.198, F:C.235, F:C.238, F:C.238

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

FES.20: 10 residues within 4Å: Chain G: C.14, W.16, M.42, C.43, T.44, C.68, C.73, H.74, Y.75, N.79 5 PLIP interactions: 5 interactions with chain G, Metal complexes: G:C.14, G:C.43, G:C.43, G:C.68, G: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: BE
CoB--CoM heterodisulfide reductase subunit B: CF
F420-non-reducing hydrogenase subunit D: G
Formate dehydrogenase, beta subunit (F420): H
Formate dehydrogenase: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
a

B
C

E
c

C
B

F
b

G
F

H
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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