SMTL ID : 8acw.1

X-ray structure of Na+-NQR from Vibrio cholerae at 3.4 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

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

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Covalent)

FMN.1: 24 residues within 4Å: Chain B: I.169, L.206, R.209, F.213, W.226, T.236, 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 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:I.169, B:E.274, B:F.338, B:M.382, B:M.383 Hydrogen bonds: B:R.209, B:R.209, B:W.226, B:T.236, B:S.239, B:S.271, B:S.271, B:G.334, B:E.380, B:E.380, B:M.382, B:M.383, B:L.384 pi-Cation interactions: B:R.209 FMN.5: 23 residues within 4Å: 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 Chain D: C.29, S.30, L.32, A.33, L.107, L.183 Chain E: S.20, F.21, F.22, L.23, S.194 16 PLIP interactions: 12 interactions with chain C, 2 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: C:W.146, C:T.173, C:L.176, D:A.33, D:L.107, E:F.22, E:L.23 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 Salt bridges: C:K.207

1 x RBF: RIBOFLAVIN(Non-covalent)

RBF.2: 25 residues within 4Å: Chain B: I.56, M.57, V.60, G.158, V.161, T.162, L.165, K.191, T.197, G.198, N.200, 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, 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

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

LMT.3: 9 residues within 4Å: Chain B: M.302, I.306, T.310, N.313, N.324, M.325, P.326, W.327, H.328 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.306, B:I.306, B:W.327, B:W.327 Hydrogen bonds: B:N.313, B:N.324, B:W.327 LMT.6: 18 residues within 4Å: Chain B: P.175, 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 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:L.181, B:F.211, D:L.155 Hydrogen bonds: B:W.177, D:Q.176, D:Q.176 LMT.8: 18 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, R.403, K.406 Chain E: F.13, V.35, K.36, F.39, M.151, L.152, V.155 12 PLIP interactions: 5 interactions with chain E, 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: E:F.13, E:L.152, E:V.155, B:F.388, B:F.392, B:F.392, B:V.399 Hydrogen bonds: E:K.36, B:K.406, A:R.429 Salt bridges: E:K.36, B:K.406

1 x K: POTASSIUM ION(Non-covalent)

K.4: 7 residues within 4Å: Chain B: M.322, I.371, R.372, N.375, P.376, Y.378, P.379 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:R.372, B:N.375, B:Y.378

1 x LYS: LYSINE(Non-covalent)

LYS.7: 4 residues within 4Å: Chain D: E.207, A.208 Chain E: P.171, R.174 1 PLIP interactions: 1 interactions with chain E, Hydrogen bonds: E:R.174

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

FES.9: 12 residues within 4Å: Chain D: G.27, C.29, S.30, T.110, 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 E, 2 interactions with chain D, Metal complexes: E:C.26, E:C.120, D:C.29, D:C.112 FES.11: 13 residues within 4Å: Chain F: L.56, S.68, A.69, C.70, G.71, 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.10: 24 residues within 4Å: Chain F: 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, A.283, D.404, F.406 19 PLIP interactions: 19 interactions with chain F Hydrophobic interactions: F:Y.167, F:A.211, F:F.406, 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:P.241, 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

2023-07-12

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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