SMTL ID : 9bp5.1

Structure of electron bifurcating Nfn-ABC holoenzyme from Caldicellulosiruptor saccharolyticus

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-mer

Ligands

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

FES.1: 11 residues within 4Å: Chain A: H.34, L.35, C.36, Y.37, G.45, A.46, C.47, G.48, C.50, R.62, C.64 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.36, A:C.47, A:C.50, A:C.64 FES.15: 8 residues within 4Å: Chain C: C.96, G.98, A.100, C.101, C.137, L.138, C.140, C.141 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.96, C:C.101, C:C.137, C:C.141 FES.16: 11 residues within 4Å: Chain D: H.34, L.35, C.36, Y.37, G.45, A.46, C.47, G.48, C.50, R.62, C.64 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.36, D:C.47, D:C.50, D:C.64 FES.30: 8 residues within 4Å: Chain F: C.96, G.98, A.100, C.101, C.137, L.138, C.140, C.141 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.96, F:C.101, F:C.137, F:C.141 FES.31: 11 residues within 4Å: Chain G: H.34, L.35, C.36, Y.37, G.45, A.46, C.47, G.48, C.50, R.62, C.64 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.36, G:C.47, G:C.50, G:C.64 FES.45: 8 residues within 4Å: Chain I: C.96, G.98, A.100, C.101, C.137, L.138, C.140, C.141 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.96, I:C.101, I:C.137, I:C.141 FES.46: 11 residues within 4Å: Chain J: H.34, L.35, C.36, Y.37, G.45, A.46, C.47, G.48, C.50, R.62, C.64 4 PLIP interactions: 4 interactions with chain J, Metal complexes: J:C.36, J:C.47, J:C.50, J:C.64 FES.60: 8 residues within 4Å: Chain L: C.96, G.98, A.100, C.101, C.137, L.138, C.140, C.141 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.96, L:C.101, L:C.137, L:C.141

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

SF4.2: 11 residues within 4Å: Chain A: C.613, I.614, L.615, C.616, G.617, L.618, C.619, V.643, C.666, P.667, A.670 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.613, A:C.616, A:C.619, A:C.666 SF4.3: 10 residues within 4Å: Chain A: H.96, G.98, D.99, C.100, C.568, Y.571, C.574, L.576, K.612, T.668 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.96, A:C.100, A:C.568, A:C.574 SF4.4: 11 residues within 4Å: Chain A: P.102, P.103, C.104, Q.115, C.155, R.156, I.164, I.166, C.563, L.564, C.566 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.104, A:C.155, A:C.563, A:C.566 SF4.5: 10 residues within 4Å: Chain A: C.108, C.114, I.143, C.147, H.149, P.150, C.151, A.167, K.170, I.481 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.108, A:C.147, A:C.151 SF4.6: 10 residues within 4Å: Chain A: I.606, C.623, L.632, C.656, I.657, S.658, C.659, G.660, Q.661, C.662 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.623, A:C.656, A:C.659, A:C.662 SF4.7: 10 residues within 4Å: Chain A: C.692, F.694, C.695, G.698, C.699, L.723, C.724, F.726, G.727, V.851 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.692, A:C.695, A:C.699, A:C.724 SF4.10: 11 residues within 4Å: Chain B: S.441, C.442, G.443, K.444, C.445, C.448, S.486, L.487, C.488, L.490, G.491 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.442, B:C.445, B:C.448, B:C.488 SF4.12: 10 residues within 4Å: Chain B: I.531, C.536, T.537, G.538, C.539, G.540, C.542, H.559, C.576, A.580 5 PLIP interactions: 5 interactions with chain B, pi-Cation interactions: B:H.559 Metal complexes: B:C.536, B:C.539, B:C.542, B:C.576 SF4.13: 13 residues within 4Å: Chain B: Y.529, C.546, T.548, A.550, I.551, I.561, C.566, T.567, K.568, C.569, G.570, T.571, C.572 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.546, B:C.566, B:C.569, B:C.572 SF4.17: 11 residues within 4Å: Chain D: C.613, I.614, L.615, C.616, G.617, L.618, C.619, V.643, C.666, P.667, A.670 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.613, D:C.616, D:C.619, D:C.666 SF4.18: 10 residues within 4Å: Chain D: H.96, G.98, D.99, C.100, C.568, Y.571, C.574, L.576, K.612, T.668 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:H.96, D:C.100, D:C.568, D:C.574 SF4.19: 11 residues within 4Å: Chain D: P.102, P.103, C.104, Q.115, C.155, R.156, I.164, I.166, C.563, L.564, C.566 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.104, D:C.155, D:C.563, D:C.566 SF4.20: 10 residues within 4Å: Chain D: C.108, C.114, I.143, C.147, H.149, P.150, C.151, A.167, K.170, I.481 3 PLIP interactions: 3 interactions with chain D, Metal complexes: D:C.108, D:C.147, D:C.151 SF4.21: 10 residues within 4Å: Chain D: I.606, C.623, L.632, C.656, I.657, S.658, C.659, G.660, Q.661, C.662 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.623, D:C.656, D:C.659, D:C.662 SF4.22: 10 residues within 4Å: Chain D: C.692, F.694, C.695, G.698, C.699, L.723, C.724, F.726, G.727, V.851 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.692, D:C.695, D:C.699, D:C.724 SF4.25: 11 residues within 4Å: Chain E: S.441, C.442, G.443, K.444, C.445, C.448, S.486, L.487, C.488, L.490, G.491 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.442, E:C.445, E:C.448, E:C.488 SF4.27: 11 residues within 4Å: Chain E: I.531, C.536, T.537, G.538, C.539, G.540, C.542, H.559, C.576, A.580, V.581 5 PLIP interactions: 5 interactions with chain E, pi-Cation interactions: E:H.559 Metal complexes: E:C.536, E:C.539, E:C.542, E:C.576 SF4.28: 13 residues within 4Å: Chain E: Y.529, C.546, T.548, A.550, I.551, I.561, C.566, T.567, K.568, C.569, G.570, T.571, C.572 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.546, E:C.566, E:C.569, E:C.572 SF4.32: 11 residues within 4Å: Chain G: C.613, I.614, L.615, C.616, G.617, L.618, C.619, V.643, C.666, P.667, A.670 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.613, G:C.616, G:C.619, G:C.666 SF4.33: 10 residues within 4Å: Chain G: H.96, G.98, D.99, C.100, C.568, Y.571, C.574, L.576, K.612, T.668 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:H.96, G:C.100, G:C.568, G:C.574 SF4.34: 11 residues within 4Å: Chain G: P.102, P.103, C.104, Q.115, C.155, R.156, I.164, I.166, C.563, L.564, C.566 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.104, G:C.155, G:C.563, G:C.566 SF4.35: 10 residues within 4Å: Chain G: C.108, C.114, I.143, C.147, H.149, P.150, C.151, A.167, K.170, I.481 3 PLIP interactions: 3 interactions with chain G, Metal complexes: G:C.108, G:C.147, G:C.151 SF4.36: 10 residues within 4Å: Chain G: I.606, C.623, L.632, C.656, I.657, S.658, C.659, G.660, Q.661, C.662 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.623, G:C.656, G:C.659, G:C.662 SF4.37: 10 residues within 4Å: Chain G: C.692, F.694, C.695, G.698, C.699, L.723, C.724, F.726, G.727, V.851 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.692, G:C.695, G:C.699, G:C.724 SF4.40: 13 residues within 4Å: Chain H: V.270, P.288, S.441, C.442, G.443, K.444, C.445, C.448, S.486, L.487, C.488, L.490, G.491 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.442, H:C.445, H:C.448, H:C.488 SF4.42: 11 residues within 4Å: Chain H: I.531, C.536, T.537, G.538, C.539, G.540, C.542, H.559, C.576, A.580, V.581 5 PLIP interactions: 5 interactions with chain H, pi-Cation interactions: H:H.559 Metal complexes: H:C.536, H:C.539, H:C.542, H:C.576 SF4.43: 13 residues within 4Å: Chain H: Y.529, C.546, T.548, A.550, I.551, I.561, C.566, T.567, K.568, C.569, G.570, T.571, C.572 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.546, H:C.566, H:C.569, H:C.572 SF4.47: 11 residues within 4Å: Chain J: C.613, I.614, L.615, C.616, G.617, L.618, C.619, V.643, C.666, P.667, A.670 4 PLIP interactions: 4 interactions with chain J, Metal complexes: J:C.613, J:C.616, J:C.619, J:C.666 SF4.48: 10 residues within 4Å: Chain J: H.96, G.98, D.99, C.100, C.568, Y.571, C.574, L.576, K.612, T.668 4 PLIP interactions: 4 interactions with chain J, Metal complexes: J:H.96, J:C.100, J:C.568, J:C.574 SF4.49: 11 residues within 4Å: Chain J: P.102, P.103, C.104, Q.115, C.155, R.156, I.164, I.166, C.563, L.564, C.566 4 PLIP interactions: 4 interactions with chain J, Metal complexes: J:C.104, J:C.155, J:C.563, J:C.566 SF4.50: 10 residues within 4Å: Chain J: C.108, C.114, I.143, C.147, H.149, P.150, C.151, A.167, K.170, I.481 3 PLIP interactions: 3 interactions with chain J, Metal complexes: J:C.108, J:C.147, J:C.151 SF4.51: 10 residues within 4Å: Chain J: I.606, C.623, L.632, C.656, I.657, S.658, C.659, G.660, Q.661, C.662 4 PLIP interactions: 4 interactions with chain J, Metal complexes: J:C.623, J:C.656, J:C.659, J:C.662 SF4.52: 10 residues within 4Å: Chain J: C.692, F.694, C.695, G.698, C.699, L.723, C.724, F.726, G.727, V.851 4 PLIP interactions: 4 interactions with chain J, Metal complexes: J:C.692, J:C.695, J:C.699, J:C.724 SF4.55: 11 residues within 4Å: Chain K: S.441, C.442, G.443, K.444, C.445, C.448, S.486, L.487, C.488, L.490, G.491 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.442, K:C.445, K:C.448, K:C.488 SF4.57: 11 residues within 4Å: Chain K: I.531, C.536, T.537, G.538, C.539, G.540, C.542, H.559, C.576, A.580, V.581 5 PLIP interactions: 5 interactions with chain K, pi-Cation interactions: K:H.559 Metal complexes: K:C.536, K:C.539, K:C.542, K:C.576 SF4.58: 12 residues within 4Å: Chain K: Y.529, C.546, A.550, I.551, I.561, C.566, T.567, K.568, C.569, G.570, T.571, C.572 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.546, K:C.566, K:C.569, K:C.572

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

FAD.8: 39 residues within 4Å: Chain A: V.146, P.148, V.198, G.199, G.200, G.201, P.202, A.203, Y.221, E.222, A.223, M.224, G.229, M.230, L.231, G.234, I.235, R.239, M.263, R.264, L.265, A.284, V.285, G.286, W.288, I.307, L.310, N.332, T.333, D.336, Q.435, R.438, D.441, G.471, D.472, K.478, I.479, A.480, A.483 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.307, A:L.310, A:N.332 Hydrogen bonds: A:V.146, A:A.203, A:A.223, A:G.229, A:M.230, A:R.239, A:R.239, A:L.265, A:W.288, A:R.438, A:D.441, A:D.472, A:K.478, A:A.480 FAD.23: 39 residues within 4Å: Chain D: V.146, P.148, V.198, G.199, G.200, G.201, P.202, A.203, Y.221, E.222, A.223, M.224, G.229, M.230, L.231, G.234, I.235, R.239, M.263, R.264, L.265, A.284, V.285, G.286, W.288, I.307, L.310, N.332, T.333, D.336, Q.435, R.438, D.441, G.471, D.472, K.478, I.479, A.480, A.483 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:I.307, D:L.310 Hydrogen bonds: D:V.146, D:A.203, D:A.223, D:G.229, D:M.230, D:R.239, D:R.239, D:L.265, D:W.288, D:R.438, D:D.441, D:D.472, D:K.478, D:A.480 FAD.38: 39 residues within 4Å: Chain G: V.146, P.148, V.198, G.199, G.200, G.201, P.202, A.203, Y.221, E.222, A.223, M.224, G.229, M.230, L.231, G.234, I.235, R.239, M.263, R.264, L.265, A.284, V.285, G.286, W.288, I.307, L.310, N.332, T.333, D.336, Q.435, R.438, D.441, G.471, D.472, K.478, I.479, A.480, A.483 16 PLIP interactions: 16 interactions with chain G Hydrophobic interactions: G:I.307, G:L.310 Hydrogen bonds: G:V.146, G:A.203, G:A.223, G:G.229, G:M.230, G:R.239, G:R.239, G:L.265, G:W.288, G:R.438, G:D.441, G:D.472, G:K.478, G:A.480 FAD.53: 39 residues within 4Å: Chain J: V.146, P.148, V.198, G.199, G.200, G.201, P.202, A.203, Y.221, E.222, A.223, M.224, G.229, M.230, L.231, G.234, I.235, R.239, M.263, R.264, L.265, A.284, V.285, G.286, W.288, I.307, L.310, N.332, T.333, D.336, Q.435, R.438, D.441, G.471, D.472, K.478, I.479, A.480, A.483 16 PLIP interactions: 16 interactions with chain J Hydrophobic interactions: J:I.307, J:L.310 Hydrogen bonds: J:V.146, J:A.203, J:A.223, J:G.229, J:M.230, J:R.239, J:R.239, J:L.265, J:W.288, J:R.438, J:D.441, J:D.472, J:K.478, J:A.480

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.9: 18 residues within 4Å: Chain B: G.153, G.155, G.156, K.164, N.181, D.183, E.184, G.185, F.269, G.272, E.273, E.274, I.307, N.308, N.309, T.312, G.489, L.490 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.269, B:E.273, B:L.490 Hydrogen bonds: B:D.183, B:G.272, B:N.308, B:N.309 Salt bridges: B:K.164 FMN.24: 18 residues within 4Å: Chain E: G.153, G.155, G.156, K.164, N.181, D.183, E.184, G.185, F.269, G.272, E.273, E.274, I.307, N.308, N.309, T.312, G.489, L.490 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:F.269, E:F.269, E:L.490 Hydrogen bonds: E:G.155, E:N.181, E:D.183, E:G.272, E:N.308, E:N.309 Salt bridges: E:K.164 FMN.39: 18 residues within 4Å: Chain H: G.153, G.155, G.156, K.164, N.181, D.183, E.184, G.185, F.269, G.272, E.273, E.274, I.307, N.308, N.309, T.312, G.489, L.490 14 PLIP interactions: 14 interactions with chain H Hydrophobic interactions: H:F.269, H:F.269, H:L.490 Hydrogen bonds: H:G.155, H:N.181, H:D.183, H:G.185, H:E.273, H:E.273, H:E.274, H:E.274, H:N.308, H:N.309 Salt bridges: H:K.164 FMN.54: 16 residues within 4Å: Chain K: G.153, G.155, G.156, K.164, N.181, D.183, E.184, G.185, F.269, G.272, E.274, I.307, N.308, N.309, G.489, L.490 8 PLIP interactions: 8 interactions with chain K Hydrophobic interactions: K:L.490 Hydrogen bonds: K:G.153, K:N.181, K:D.183, K:G.185, K:G.272, K:N.309 Salt bridges: K:K.164

8 x ZN: ZINC ION(Non-covalent)

ZN.11: 4 residues within 4Å: Chain B: C.10, C.41, C.45, E.48 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.10, B:C.41, B:C.45, B:E.48 ZN.14: 4 residues within 4Å: Chain B: C.425, H.512, C.518, C.523 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.425, B:H.512, B:C.518, B:C.523 ZN.26: 4 residues within 4Å: Chain E: C.10, C.41, C.45, E.48 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.10, E:C.41, E:C.45, E:E.48 ZN.29: 4 residues within 4Å: Chain E: C.425, H.512, C.518, C.523 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.425, E:H.512, E:C.518, E:C.523 ZN.41: 4 residues within 4Å: Chain H: C.10, C.41, C.45, E.48 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.10, H:C.41, H:C.45, H:E.48 ZN.44: 4 residues within 4Å: Chain H: C.425, H.512, C.518, C.523 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.425, H:H.512, H:C.518, H:C.523 ZN.56: 4 residues within 4Å: Chain K: C.10, C.41, C.45, E.48 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.10, K:C.41, K:C.45, K:E.48 ZN.59: 4 residues within 4Å: Chain K: C.425, H.512, C.518, C.523 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.425, K:H.512, K:C.518, K:C.523

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, H. et al., Cryo-EM reveals a composite flavobicluster electron bifurcation site in the Bfu family member NfnABC. Commun Biol (2025)

Release Date

2025-03-05

Peptides

Molybdopterin oxidoreductase: ADGJ
NADH dehydrogenase (Quinone): BEHK
NADH dehydrogenase (Ubiquinone), 24 kDa subunit: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

G
G

J
J

B
B

E
E

H
H

K
K

C
C

F
F

I
I

L
L

Molybdopterin oxidoreductase

NADH dehydrogenase (Quinone)

NADH dehydrogenase (Ubiquinone), 24 kDa subunit

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