SMTL ID : 9n5v.1

Structure of the NAD(H)-bound Thermococcus sibiricus NfnABC complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.76 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: C.640, V.641, L.642, C.643, G.644, C.646, I.670, C.693, P.694, V.695, A.697, I.698 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.640, A:C.643, A:C.646, A:C.693 SF4.2: 10 residues within 4Å: Chain A: C.111, V.117, Y.120, Y.140, L.146, C.150, F.153, C.154, K.173, I.483 4 PLIP interactions: 4 interactions with chain A, pi-Cation interactions: A:Y.140 Metal complexes: A:C.111, A:C.150, A:C.154 SF4.3: 10 residues within 4Å: Chain A: P.106, C.107, Q.118, L.121, C.158, R.159, I.169, C.590, M.591, C.593 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.107, A:C.158, A:C.590, A:C.593 SF4.4: 10 residues within 4Å: Chain A: H.99, G.101, D.102, C.103, H.539, C.595, V.598, C.601, K.639, V.695 5 PLIP interactions: 5 interactions with chain A, Metal complexes: A:H.99, A:H.99, A:C.103, A:C.595, A:C.601 SF4.6: 10 residues within 4Å: Chain A: C.719, G.721, C.722, F.724, A.725, C.726, I.751, C.752, C.755, L.849 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.719, A:C.722, A:C.726, A:C.752 SF4.8: 12 residues within 4Å: Chain B: V.282, P.300, S.453, C.454, G.455, K.456, C.457, C.460, S.498, C.500, L.502, G.503 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.454, B:C.457, B:C.460, B:C.500 SF4.10: 9 residues within 4Å: Chain B: I.542, C.547, T.548, C.550, C.553, C.587, R.588, A.591, I.592 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.547, B:C.550, B:C.553 SF4.11: 11 residues within 4Å: Chain B: Y.540, C.557, V.559, I.572, C.577, I.578, K.579, C.580, G.581, T.582, C.583 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.557, B:C.577, B:C.580

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

FAD.5: 35 residues within 4Å: Chain A: V.149, P.151, V.201, G.202, G.203, G.204, P.205, A.206, D.225, A.226, M.227, G.231, G.232, M.233, I.238, R.242, A.267, L.268, G.287, V.288, G.289, W.291, L.313, N.335, T.336, D.339, N.365, Q.436, F.442, G.473, D.474, S.480, T.481, V.482, S.485 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:N.335, A:V.482 Hydrogen bonds: A:G.203, A:A.206, A:A.226, A:M.227, A:M.233, A:L.268, A:L.268, A:W.291, A:D.474, A:S.480, A:S.485 pi-Stacking: A:W.291

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

FES.7: 11 residues within 4Å: Chain A: I.28, G.39, C.41, Y.42, Y.49, G.50, C.52, R.53, C.55, T.65, C.67 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.41, A:C.52, A:C.55, A:C.67

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.9: 19 residues within 4Å: Chain B: G.165, R.166, G.167, K.176, N.193, D.195, E.196, G.197, F.281, G.284, E.285, E.286, I.319, N.320, N.321, T.324, G.501, L.502 Ligands: NAD.12 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.281, B:E.285, B:L.502 Hydrogen bonds: B:G.167, B:N.193, B:N.193, B:G.197, B:E.286, B:N.320, B:N.321, B:N.321, B:T.324 Salt bridges: B:K.176

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

NAD.12: 17 residues within 4Å: Chain B: G.167, G.168, A.169, F.171, K.176, F.179, F.281, E.286, R.303, Y.306, P.307, A.308, Q.309, I.423, G.425, S.426 Ligands: FMN.9 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.286, B:Q.309, B:G.425 Salt bridges: B:R.303, B:R.303 pi-Stacking: B:F.171, B:Y.306

2 x ZN: ZINC ION(Non-covalent)

ZN.13: 4 residues within 4Å: Chain B: C.437, H.524, C.529, C.534 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.437, B:H.524, B:C.529, B:C.534 ZN.14: 5 residues within 4Å: Chain B: C.14, C.45, C.49, E.52, N.206 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.14, B:C.45, B:C.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiao, X. et al., Cryo-EM structures define the electron bifurcating flavobicluster and ferredoxin binding site in an archaeal Nfn-Bfu transhydrogenase. J.Biol.Chem. (2025)

Release Date

2025-05-07

Peptides

NfnA: A
NfnB: B
NfnC: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

NfnA

NfnB

NfnC

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