SMTL ID : 8ad0.1

X-ray structure of Na+-NQR from Vibrio cholerae in different conformation at 3.1 A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.11 Å

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 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:I.169, B:L.206, B:E.274, B:M.382, B:M.383 Hydrogen bonds: B:R.209, B:R.209, B:L.238, B:S.239, 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 pi-Cation interactions: B:R.209 FMN.7: 20 residues within 4Å: Chain B: F.213, F.214, P.217, S.221, 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, S.228 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:P.217, C:L.176 Hydrogen bonds: B:A.377, C:W.146, C:G.223, 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: 27 residues within 4Å: Chain A: V.397 Chain B: I.56, M.57, V.60, G.158, V.161, T.162, L.165, K.191, G.196, T.197, G.198, R.199, 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 9 PLIP interactions: 9 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.203, B:N.203, B:A.205, B:D.346

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, V.314, N.324, P.326, W.327, H.328 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.306, B:W.327 Hydrogen bonds: B:N.324, B:N.324, B:W.327 LMT.9: 19 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, F.193 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:L.155, D:F.189, B:L.181, B:F.211 Hydrogen bonds: D:W.174, D:W.174, D:Q.176, D:Q.176, B:W.177 LMT.11: 19 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 Ligands: 3PE.4 13 PLIP interactions: 5 interactions with chain E, 8 interactions with chain B Hydrophobic interactions: E:F.13, E:L.152, E:V.155, B:F.388, B:F.392, B:L.395, B:F.396, B:F.396 Hydrogen bonds: E:K.36, B:E.402, B:K.406 Salt bridges: E:K.36, B:K.406

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

3PE.4: 14 residues within 4Å: Chain A: K.28 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.11 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.307, B:W.358, B:I.362 Hydrogen bonds: B:R.296 Salt bridges: B:R.296

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

NA.5: 8 residues within 4Å: Chain B: A.263, I.268, E.274, V.275, T.277, V.332, L.333, G.334 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.263 Water bridges: B:G.334

1 x K: POTASSIUM ION(Non-covalent)

K.6: 2 residues within 4Å: Chain B: A.242, P.376 No protein-ligand interaction detected (PLIP)

1 x BR: BROMIDE ION(Non-covalent)

BR.8: 6 residues within 4Å: Chain C: Q.93, A.97, R.118, A.119, H.141, W.238 Ligand excluded by PLIP

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

FES.10: 12 residues within 4Å: Chain D: G.27, V.28, C.29, T.110, N.111, C.112 Chain E: G.24, M.25, C.26, V.118, 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.13: 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.12: 26 residues within 4Å: Chain F: 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, S.247, A.283, A.286, D.404, D.405, F.406 20 PLIP interactions: 20 interactions with chain F Hydrophobic interactions: F:Y.167, F:A.211, F:F.406, F:F.406 Hydrogen bonds: F:A.211, F:A.211, F:Y.212, F:S.213, F:N.227, F:R.229, F:T.232, F:N.237, F:P.241, F:Q.244, F:M.245, F:S.246, F:S.246 Salt bridges: F:R.210, F:R.210 pi-Stacking: F:Y.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fritz, G., X-ray structure of Na+-NQR from Vibrio cholerae at 3.4 A resolution. 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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