SMTL ID : 8a1u.1

Sodium pumping NADH-quinone oxidoreductase with substrates NADH and Q2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Covalent)

FMN.1: 25 residues within 4Å: Chain B: I.169, L.206, R.209, F.213, W.226, T.236, A.237, L.238, S.239, G.270, S.271, E.274, G.334, G.335, F.338, G.339, M.343, Y.378, P.379, E.380, G.381, M.382, M.383, L.384, I.386 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.169, B:E.274, B:M.383 Hydrogen bonds: B:L.238, B:S.239, B:S.271, B:S.271, B:E.274, B:G.335, B:E.380, B:E.380, B:M.382, B:M.383, B:L.384 Water bridges: B:A.237, B:S.239 pi-Cation interactions: B:R.209 FMN.11: 23 residues within 4Å: Chain B: F.213, F.214, P.217, I.220, S.221, G.222, D.223, Q.243, A.377, Y.378, P.379 Chain C: L.145, W.146, E.172, T.173, L.176, G.177, K.207, G.223, A.224, T.225, L.226, T.227 17 PLIP interactions: 7 interactions with chain B, 10 interactions with chain C Hydrophobic interactions: B:F.213, B:F.214, B:P.217, B:Y.378, C:W.146 Hydrogen bonds: B:G.222, B:D.223, B:Q.243, C:W.146, C:T.173, C:T.173, C:T.225, C:L.226, C:T.227, C:T.227 Water bridges: C:G.223 Salt bridges: C:K.207

1 x RBF: RIBOFLAVIN(Non-covalent)

RBF.2: 29 residues within 4Å: Chain A: V.397, I.399 Chain B: I.56, M.57, V.60, G.158, V.161, T.162, L.165, K.191, T.197, G.198, R.199, N.200, L.202, N.203, P.204, A.205, L.206, I.287, I.292, A.293, F.342, M.343, T.345, D.346, P.347, V.348, S.349 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.56, B:V.60 Hydrogen bonds: B:T.162, B:G.198, B:N.200, B:N.200, B:N.203, B:N.203, B:A.205, B:D.346

3 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.3: 17 residues within 4Å: Chain A: R.429 Chain B: L.363, F.388, F.392, L.395, F.396, H.398, V.399, E.402, K.406 Chain E: F.13, V.35, K.36, F.39, L.152, V.155 Ligands: 3PE.4 8 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: B:F.388, B:F.392, B:V.399, E:L.152 Hydrogen bonds: B:H.398, B:E.402, A:R.429 Salt bridges: B:H.398 LMT.5: 9 residues within 4Å: Chain B: M.302, I.306, T.310, N.313, N.324, P.326, W.327, H.328 Ligands: 3PE.6 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.306, B:I.306, B:W.327, B:W.327, B:W.327 Hydrogen bonds: B:N.313, B:N.324, B:W.327 Water bridges: B:W.327 LMT.13: 19 residues within 4Å: Chain B: W.177, L.181, F.185, V.189, F.211, Y.216 Chain D: L.155, I.169, W.174, Y.175, Q.176, N.178, L.180, M.181, S.186, F.189, L.190, F.193 Ligands: 3PE.12 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: B:L.181, D:L.155, D:F.189, D:F.189 Hydrogen bonds: D:W.174, D:Q.176

4 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.4: 13 residues within 4Å: Chain B: W.295, R.296, I.303, L.307, N.354, S.355, W.358, A.359, I.362, L.363, V.366, F.396 Ligands: LMT.3 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.362, B:I.362, B:L.363, B:L.363 Hydrogen bonds: B:N.354 Salt bridges: B:R.296 3PE.6: 11 residues within 4Å: Chain B: W.260, M.261, F.264, M.281, M.302, P.326, W.327, H.328, W.329, L.331 Ligands: LMT.5 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.260, B:W.260, B:F.264, B:F.264, B:W.327, B:H.328 Salt bridges: B:H.328 3PE.8: 24 residues within 4Å: Chain B: W.61, F.65, M.68, F.69, M.72, W.100, L.104, L.108, G.109, G.110, T.111, G.117, W.118, G.119, S.120, M.122, L.123, A.126, T.127, F.129, L.130, P.131, Y.133, I.164 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.69, B:W.100, B:L.108, B:L.123, B:A.126, B:T.127, B:L.130, B:L.130 Hydrogen bonds: B:T.111, B:G.117, B:G.119, B:S.120, B:S.120 3PE.12: 19 residues within 4Å: Chain B: W.143, L.146, F.147, V.150, R.151, L.181, T.184, F.185, V.188, V.189, F.211 Chain D: L.190, F.193, W.196, A.197, T.200 Chain E: P.170, P.171 Ligands: LMT.13 11 PLIP interactions: 4 interactions with chain D, 7 interactions with chain B Hydrophobic interactions: D:F.193, D:F.193, D:W.196, D:A.197, B:W.143, B:F.147, B:L.181, B:T.184, B:F.185, B:V.189 Hydrogen bonds: B:R.151

1 x UQ2: UBIQUINONE-2(Non-covalent)

UQ2.7: 15 residues within 4Å: Chain B: L.26, A.29, A.30, L.33, F.137, I.138, G.141, F.142, E.144, V.145, V.155, N.156, E.157, F.159, F.160 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.26, B:F.137, B:F.142, B:V.155, B:F.159

2 x NA: SODIUM ION(Non-functional Binders)

NA.9: 7 residues within 4Å: Chain B: A.263, G.266, I.268, E.274, V.275, T.277, V.332 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.274 NA.10: 6 residues within 4Å: Chain B: I.371, R.372, N.375, P.376, Y.378, P.379 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.371

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

FES.14: 12 residues within 4Å: Chain D: L.26, G.27, V.28, C.29, N.111, C.112 Chain E: G.24, M.25, C.26, T.27, N.119, C.120 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain E, Metal complexes: D:C.29, D:C.112, E:C.26, E:C.120 FES.16: 13 residues within 4Å: Chain F: L.56, S.68, C.70, G.71, G.72, G.74, S.75, C.76, G.77, Q.78, C.79, L.109, C.111 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.70, F:C.76, F:C.79, F:C.111

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

FAD.15: 24 residues within 4Å: Chain F: A.69, Y.167, R.210, A.211, Y.212, S.213, N.227, V.228, R.229, A.231, T.232, P.233, P.234, N.237, V.240, P.241, P.242, G.243, Q.244, M.245, S.246, A.283, F.406 Ligands: NAI.17 20 PLIP interactions: 20 interactions with chain F Hydrophobic interactions: F:A.69, F:Y.167, F:A.211, F:F.406 Hydrogen bonds: F:A.211, F:Y.212, F:Y.212, F:S.213, F:N.227, F:R.229, F:T.232, F:P.241, F:Q.244, F:Q.244, F:M.245, F:S.246 Salt bridges: F:R.210, F:R.210 pi-Stacking: F:Y.212, F:Y.212

1 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.17: 24 residues within 4Å: Chain F: S.213, R.229, G.281, G.282, A.283, G.284, P.287, G.310, A.311, R.312, S.340, F.354, I.355, H.356, C.378, G.379, P.380, P.381, M.382, M.383, A.386, D.404, F.406 Ligands: FAD.15 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:A.283 Hydrogen bonds: F:R.229, F:A.283, F:S.340, F:S.340, F:D.404 Salt bridges: F:R.312

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hau, J.L. et al., Conformational coupling of redox-driven Na + -translocation in Vibrio cholerae NADH:quinone oxidoreductase. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-09-20

Peptides

Na(+)-translocating NADH-quinone reductase subunit A: A
Na(+)-translocating NADH-quinone reductase subunit B: B
Na(+)-translocating NADH-quinone reductase subunit C: C
Na(+)-translocating NADH-quinone reductase subunit D: D
Na(+)-translocating NADH-quinone reductase subunit E: E
Na(+)-translocating NADH-quinone reductase subunit F: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Membrane

We predict this structure to be a membrane protein.
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Na(+)-translocating NADH-quinone reductase subunit A

Na(+)-translocating NADH-quinone reductase subunit B

Na(+)-translocating NADH-quinone reductase subunit C

Na(+)-translocating NADH-quinone reductase subunit D

Na(+)-translocating NADH-quinone reductase subunit E

Na(+)-translocating NADH-quinone reductase subunit F

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