SMTL ID : 8ad4.1 (1 other biounit)

X-ray structure of NqrF(129-408)of Vibrio cholerae in complex with NADH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

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

FAD.1: 25 residues within 4Å: Chain A: Y.42, R.85, A.86, Y.87, S.88, N.102, V.103, R.104, A.106, T.107, P.108, P.109, N.112, V.115, P.116, P.117, G.118, Q.119, M.120, S.121, S.122, A.158, A.161, D.279, F.281 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:Y.42, A:A.86, A:F.281, A:F.281 Hydrogen bonds: A:A.86, A:A.86, A:Y.87, A:S.88, A:S.88, A:N.102, A:R.104, A:A.106, A:P.116, A:Q.119, A:M.120, A:S.121, A:S.121 Water bridges: A:R.85, A:R.85, A:R.85, A:R.85, A:N.102, A:T.107 Salt bridges: A:R.85, A:R.85 pi-Stacking: A:F.281

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

NAI.2: 24 residues within 4Å: Chain A: R.104, G.156, G.157, A.158, G.159, G.185, A.186, R.187, S.215, G.228, F.229, I.230, H.231, C.253, G.254, P.255, P.256, M.257, M.258, A.261, D.279, D.280, F.281, G.282 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.281 Hydrogen bonds: A:R.104, A:R.104, A:A.158, A:R.187, A:S.215, A:I.230, A:G.254, A:D.279, A:F.281 Water bridges: A:R.104, A:R.104, A:A.186, A:G.228, A:H.231, A:G.282 Salt bridges: A:R.187 pi-Stacking: A:F.229 NAI.3: 14 residues within 4Å: Chain A: F.21, D.66, K.69, F.70, L.72, Y.75, R.104, I.105, A.106, T.107, P.108, P.110, R.187, D.216 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.21, A:F.21, A:F.70 Hydrogen bonds: A:D.66, A:R.104, A:I.105, A:T.107, A:T.107 Water bridges: A:R.187 Salt bridges: A:K.69, A:K.69

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

NA.4: 7 residues within 4Å: Chain A: K.18, A.19, K.62, Y.63, R.190, M.192, F.193 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.63 Water bridges: A:Y.63 NA.5: 5 residues within 4Å: Chain A: A.202, N.205, D.206, F.208, V.209 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.208, A:F.208

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 5 residues within 4Å: Chain A: K.18, F.193, Y.194, V.195, E.196 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.194, A:V.195, A:E.196 Water bridges: A:M.192 Salt bridges: A:K.18

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 F: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

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

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