SMTL ID : 9bov.1

Structure of electron bifurcating Nfn-ABC complexed with NAD from Caldicellulosiruptor saccharolyticus

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-mer

Ligands

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

FES.1: 9 residues within 4Å: Chain A: H.34, L.35, C.36, Y.37, G.45, C.47, G.48, C.50, 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.13: 9 residues within 4Å: Chain D: H.34, L.35, C.36, Y.37, G.45, C.47, G.48, C.50, 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.25: 9 residues within 4Å: Chain G: H.34, L.35, C.36, Y.37, G.45, C.47, G.48, C.50, 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.37: 9 residues within 4Å: Chain J: H.34, L.35, C.36, Y.37, G.45, C.47, G.48, C.50, C.64 4 PLIP interactions: 4 interactions with chain J, Metal complexes: J:C.36, J:C.47, J:C.50, J:C.64

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

SF4.2: 12 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, T.668, 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: 9 residues within 4Å: Chain A: H.96, G.98, D.99, C.100, C.568, Y.571, C.574, 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: 10 residues within 4Å: Chain A: P.102, P.103, C.104, Q.115, C.155, R.156, 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: 12 residues within 4Å: Chain A: C.108, P.109, C.114, Y.117, 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: 9 residues within 4Å: Chain A: I.606, C.623, L.632, C.656, I.657, S.658, C.659, G.660, 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: V.270, S.441, C.442, G.443, K.444, C.445, C.448, S.486, 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 SF4.14: 12 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, T.668, A.670 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.613, D:C.616, D:C.619, D:C.666 SF4.15: 9 residues within 4Å: Chain D: H.96, G.98, D.99, C.100, C.568, Y.571, C.574, 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 SF4.16: 10 residues within 4Å: Chain D: P.102, P.103, C.104, Q.115, C.155, R.156, 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 SF4.17: 12 residues within 4Å: Chain D: C.108, P.109, C.114, Y.117, 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 SF4.18: 9 residues within 4Å: Chain D: I.606, C.623, L.632, C.656, I.657, S.658, C.659, G.660, C.662 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.623, D:C.656, D:C.659, D:C.662 SF4.19: 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 SF4.22: 11 residues within 4Å: Chain E: V.270, S.441, C.442, G.443, K.444, C.445, C.448, S.486, 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 SF4.26: 12 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, T.668, A.670 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.613, G:C.616, G:C.619, G:C.666 SF4.27: 9 residues within 4Å: Chain G: H.96, G.98, D.99, C.100, C.568, Y.571, C.574, 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 SF4.28: 10 residues within 4Å: Chain G: P.102, P.103, C.104, Q.115, C.155, R.156, 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 SF4.29: 12 residues within 4Å: Chain G: C.108, P.109, C.114, Y.117, 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 SF4.30: 9 residues within 4Å: Chain G: I.606, C.623, L.632, C.656, I.657, S.658, C.659, G.660, C.662 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.623, G:C.656, G:C.659, G:C.662 SF4.31: 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 SF4.34: 11 residues within 4Å: Chain H: V.270, S.441, C.442, G.443, K.444, C.445, C.448, S.486, 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 SF4.38: 12 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, T.668, A.670 4 PLIP interactions: 4 interactions with chain J, Metal complexes: J:C.613, J:C.616, J:C.619, J:C.666 SF4.39: 9 residues within 4Å: Chain J: H.96, G.98, D.99, C.100, C.568, Y.571, C.574, 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 SF4.40: 10 residues within 4Å: Chain J: P.102, P.103, C.104, Q.115, C.155, R.156, 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 SF4.41: 12 residues within 4Å: Chain J: C.108, P.109, C.114, Y.117, 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 SF4.42: 9 residues within 4Å: Chain J: I.606, C.623, L.632, C.656, I.657, S.658, C.659, G.660, C.662 4 PLIP interactions: 4 interactions with chain J, Metal complexes: J:C.623, J:C.656, J:C.659, J:C.662 SF4.43: 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 SF4.46: 11 residues within 4Å: Chain K: V.270, S.441, C.442, G.443, K.444, C.445, C.448, S.486, 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

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

FAD.8: 38 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, 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 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.235, A:I.307, A:L.310, A:N.332 Hydrogen bonds: A:V.146, A:G.200, A:A.203, A:A.223, A:M.224, 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.20: 38 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, 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 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:I.307, D:L.310, D:N.332 Hydrogen bonds: D:V.146, D:G.200, D:A.203, D:A.223, D:M.224, 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.32: 38 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, 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 19 PLIP interactions: 19 interactions with chain G Hydrophobic interactions: G:I.307, G:L.310, G:N.332 Hydrogen bonds: G:V.146, G:G.200, G:A.203, G:A.223, G:M.224, 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.44: 38 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, 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 19 PLIP interactions: 19 interactions with chain J Hydrophobic interactions: J:I.307, J:L.310, J:N.332 Hydrogen bonds: J:V.146, J:G.200, J:A.203, J:A.223, J:M.224, 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, A.157, K.164, N.181, D.183, E.184, F.269, G.272, E.273, E.274, I.307, N.308, N.309, T.312, G.489, L.490 Ligands: NAD.12 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.490 Hydrogen bonds: B:G.155, B:N.181, B:N.181, B:E.274, B:N.308, B:N.309 Salt bridges: B:K.164 FMN.21: 18 residues within 4Å: Chain E: G.153, G.155, A.157, K.164, N.181, D.183, E.184, F.269, G.272, E.273, E.274, I.307, N.308, N.309, T.312, G.489, L.490 Ligands: NAD.24 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:F.269, E:L.490 Hydrogen bonds: E:G.155, E:N.181, E:N.181, E:G.185, E:E.274, E:N.308, E:N.309 Salt bridges: E:K.164 FMN.33: 18 residues within 4Å: Chain H: G.153, G.155, A.157, K.164, N.181, D.183, E.184, F.269, G.272, E.273, E.274, I.307, N.308, N.309, T.312, G.489, L.490 Ligands: NAD.36 11 PLIP interactions: 11 interactions with chain H Hydrophobic interactions: H:F.269, H:L.490 Hydrogen bonds: H:G.155, H:N.181, H:N.181, H:E.184, H:G.185, H:E.274, H:N.308, H:N.309 Salt bridges: H:K.164 FMN.45: 18 residues within 4Å: Chain K: G.153, G.155, A.157, K.164, N.181, D.183, E.184, F.269, G.272, E.273, E.274, I.307, N.308, N.309, T.312, G.489, L.490 Ligands: NAD.48 10 PLIP interactions: 10 interactions with chain K Hydrophobic interactions: K:F.269, K:L.490 Hydrogen bonds: K:G.155, K:N.181, K:N.181, K:G.185, K:E.274, K:N.308, K:N.309 Salt bridges: K:K.164

4 x ZN: ZINC ION(Non-covalent)

ZN.11: 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.23: 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.35: 5 residues within 4Å: Chain H: C.425, H.512, C.518, C.523, L.526 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.425, H:H.512, H:C.518, H:C.523 ZN.47: 5 residues within 4Å: Chain K: C.425, D.428, 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

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.12: 18 residues within 4Å: Chain B: G.155, G.156, A.157, F.159, K.164, D.186, F.269, E.273, E.274, K.291, F.294, P.295, A.296, S.387, I.411, G.413, S.414 Ligands: FMN.9 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.269 Hydrogen bonds: B:G.155, B:K.164, B:E.273, B:E.274 Salt bridges: B:K.291 pi-Stacking: B:F.159, B:F.294, B:F.294 NAD.24: 17 residues within 4Å: Chain E: G.155, G.156, A.157, F.159, K.164, D.186, F.269, E.274, K.291, F.294, P.295, A.296, S.387, I.411, G.413, S.414 Ligands: FMN.21 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:F.269 Hydrogen bonds: E:E.274 Salt bridges: E:K.291, E:K.291 pi-Stacking: E:F.159, E:F.294, E:F.294 NAD.36: 17 residues within 4Å: Chain H: G.155, G.156, A.157, F.159, K.164, D.186, F.269, E.274, K.291, F.294, P.295, A.296, S.387, I.411, G.413, S.414 Ligands: FMN.33 7 PLIP interactions: 7 interactions with chain H Hydrophobic interactions: H:F.269 Hydrogen bonds: H:E.274 Salt bridges: H:K.291, H:K.291 pi-Stacking: H:F.159, H:F.294, H:F.294 NAD.48: 17 residues within 4Å: Chain K: G.155, G.156, A.157, F.159, K.164, D.186, F.269, E.274, K.291, F.294, P.295, A.296, S.387, I.411, G.413, S.414 Ligands: FMN.45 7 PLIP interactions: 7 interactions with chain K Hydrophobic interactions: K:F.269 Hydrogen bonds: K:E.274 Salt bridges: K:K.291, K:K.291 pi-Stacking: K:F.159, K:F.294, K:F.294

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
J

J
G

B
B

E
E

H
K

K
H

C
C

F
F

I
L

L
I

Molybdopterin oxidoreductase

NADH dehydrogenase (Quinone)

NADH dehydrogenase (Ubiquinone), 24 kDa subunit

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