SMTL ID : 8a1v.1

Sodium pumping NADH-quinone oxidoreductase with substrate Q2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x RBF: RIBOFLAVIN(Non-covalent)

RBF.1: 28 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 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.56, B:V.60, B:P.347 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 Water bridges: B:G.158, B:T.162

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

3PE.2: 20 residues within 4Å: Chain B: W.143, L.146, F.147, V.150, R.151, H.153, T.184, F.185, V.188, V.189 Chain D: F.189, L.190, F.193, W.196, A.197, T.200 Chain E: D.168, P.170, P.171 Ligands: LMT.10 18 PLIP interactions: 10 interactions with chain B, 8 interactions with chain D Hydrophobic interactions: B:W.143, B:F.147, B:F.147, B:T.184, B:V.188, B:V.189, D:F.193, D:F.193, D:F.193, D:W.196, D:W.196, D:W.196, D:T.200 Hydrogen bonds: B:R.151, B:R.151, B:H.153, D:W.196 Salt bridges: B:R.151 3PE.4: 10 residues within 4Å: Chain B: W.260, M.261, F.264, M.281, P.326, W.327, H.328, W.329, L.331 Ligands: LMT.3 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.260, B:W.260, B:F.264, B:L.331 Hydrogen bonds: B:H.328 Water bridges: B:M.261, B:H.328 Salt bridges: B:H.328

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

LMT.3: 11 residues within 4Å: Chain B: M.302, I.306, T.310, N.313, V.314, N.324, M.325, P.326, W.327, H.328 Ligands: 3PE.4 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.306, B:W.327, B:W.327 Hydrogen bonds: B:N.313, B:N.324 Water bridges: B:W.327, B:W.327, B:H.328, B:H.328 LMT.10: 17 residues within 4Å: Chain B: P.175, W.177, L.181, F.185, 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 Ligands: 3PE.2 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: B:L.181, B:F.211, D:L.155, D:F.189 Hydrogen bonds: B:W.177, D:W.174, D:Q.176, D:Q.176 Water bridges: B:Q.178, B:Q.178 LMT.11: 15 residues within 4Å: 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 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: B:L.363, B:F.388, B:F.392, B:F.392, B:L.395, B:F.396, B:V.399, E:L.152 Hydrogen bonds: B:K.406 Water bridges: B:H.398

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

UQ2.5: 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 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.26, B:F.137, B:I.138, B:F.142, B:F.142, B:E.144, B:V.145, B:V.145, B:F.159

2 x FMN: FLAVIN MONONUCLEOTIDE(Covalent)

FMN.6: 24 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 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:I.169, B:E.274, B:M.382, B:M.383 Hydrogen bonds: B:R.209, 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:R.209, B:W.226, B:W.226, B:A.237, B:G.334 pi-Cation interactions: B:R.209 FMN.9: 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 18 PLIP interactions: 11 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: C:W.146, C:L.176, B:F.213, B:F.214, B:P.217 Hydrogen bonds: C:W.146, C:T.173, C:T.173, C:G.177, C:T.225, C:L.226, C:T.227, C:T.227, B:G.222, B:D.223, B:Q.243 Salt bridges: C:K.207 Water bridges: B:D.223

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

NA.7: 6 residues within 4Å: Chain B: A.263, G.266, I.268, V.275, T.277, V.332 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.277, B:V.332 NA.8: 6 residues within 4Å: Chain B: I.371, R.372, N.375, P.376, Y.378, P.379 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.372, B:N.375

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

FES.12: 11 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, 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.14: 12 residues within 4Å: Chain F: S.68, C.70, G.72, G.74, S.75, C.76, G.77, Q.78, C.79, L.109, C.111, Q.112 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.13: 25 residues within 4Å: Chain F: A.69, Q.78, Y.167, I.208, R.210, A.211, Y.212, S.213, N.227, V.228, R.229, A.231, T.232, P.233, P.234, V.240, P.241, P.242, G.243, Q.244, M.245, S.246, S.247, A.283, F.406 19 PLIP interactions: 19 interactions with chain F Hydrophobic interactions: F:Y.167, F:A.211, F:F.406 Hydrogen bonds: F:A.211, F:Y.212, F:S.213, F:N.227, F:R.229, F:T.232, F:T.232, F:T.232, F:Q.244, F:Q.244, F:Q.244, F:M.245, F:S.246, F:S.246 Salt bridges: F:R.210, F:R.210

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

2023-06-14

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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