SMTL ID : 4ykf.1

Crystal Structure of the Alkylhydroperoxide Reductase subunit F (AhpF) with NADH from Escherichia coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 34 residues within 4Å: Chain A: V.218, G.219, S.220, G.221, P.222, A.223, G.242, E.243, R.244, G.247, Q.248, I.249, D.251, T.252, D.254, I.255, N.257, Q.288, S.289, A.290, A.321, T.322, G.323, A.324, C.348, N.454, W.457, G.487, D.488, K.495, Q.496, I.497, A.500 Chain B: Y.230 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:S.220, A:G.221, A:A.223, A:E.243, A:E.243, A:R.244, A:G.247, A:Q.248, A:T.252, A:N.257, A:N.257, A:A.290, A:A.290, A:A.324, A:D.488, A:K.495, A:I.497 Water bridges: A:G.224, A:R.244, A:N.257, A:N.257, A:G.323, A:I.498 FAD.20: 34 residues within 4Å: Chain A: Y.230 Chain B: V.218, G.219, S.220, G.221, P.222, A.223, G.242, E.243, R.244, G.247, Q.248, I.249, D.251, T.252, D.254, I.255, N.257, Q.288, S.289, A.290, A.321, T.322, G.323, A.324, C.348, N.454, W.457, G.487, D.488, K.495, Q.496, I.497, A.500 24 PLIP interactions: 23 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.220, B:G.221, B:A.223, B:E.243, B:E.243, B:R.244, B:G.247, B:Q.248, B:N.257, B:N.257, B:A.290, B:A.290, B:A.324, B:D.488, B:K.495, B:I.497, A:Y.230 Water bridges: B:G.224, B:R.244, B:T.252, B:N.257, B:N.257, B:G.323, B:I.498

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

NAI.2: 16 residues within 4Å: Chain A: I.361, G.362, G.363, G.364, N.365, S.366, E.369, L.384, E.385, F.386, K.391, I.449, G.450, M.467 Chain B: K.475, D.513 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:N.365 Hydrogen bonds: A:G.362, A:G.363, A:G.363, A:S.366, A:S.366, A:F.386, A:K.391, B:K.475, B:K.475 Water bridges: A:M.329, A:G.364, A:G.364, A:S.366, A:T.414, A:Q.448, A:L.451 Salt bridges: A:K.391 NAI.21: 16 residues within 4Å: Chain A: K.475, D.513 Chain B: I.361, G.362, G.363, G.364, N.365, S.366, E.369, L.384, E.385, F.386, K.391, I.449, G.450, M.467 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:N.365 Hydrogen bonds: B:G.362, B:G.363, B:G.363, B:S.366, B:S.366, B:F.386, B:K.391, A:K.475, A:K.475 Water bridges: B:M.329, B:G.364, B:G.364, B:S.366, B:T.414, B:Q.448, B:L.451 Salt bridges: B:K.391

2 x CD: CADMIUM ION(Non-covalent)

CD.3: 2 residues within 4Å: Chain A: H.85, H.130 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.85, A:H.130 CD.22: 2 residues within 4Å: Chain B: H.85, H.130 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.85, B:H.130

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

SO4.4: 5 residues within 4Å: Chain A: P.453, N.454, T.455, N.456, W.457 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: I.437, H.438, N.439 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: P.332, G.333, E.334, D.335, Q.336 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: D.393, Q.394, V.395 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: D.473, A.474 Ligands: SO4.27 Ligand excluded by PLIP SO4.9: 2 residues within 4Å: Chain A: R.357, H.380 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain A: R.357, N.439, I.440, E.441 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain A: R.210, D.211, R.237, D.283 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain A: R.517 Chain B: V.395 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain A: Q.413, R.430, R.432 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain B: P.453, N.454, T.455, N.456, W.457 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain B: I.437, H.438, N.439 Ligand excluded by PLIP SO4.25: 5 residues within 4Å: Chain B: P.332, G.333, E.334, D.335, Q.336 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain B: D.393, Q.394, V.395 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain B: D.473, A.474 Ligands: SO4.8 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain B: R.357, H.380 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain B: R.357, N.439, I.440, E.441 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain B: R.210, D.211, R.237, D.283 Ligand excluded by PLIP SO4.31: 2 residues within 4Å: Chain A: V.395 Chain B: R.517 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain B: Q.413, R.430, R.432 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 4 residues within 4Å: Chain A: K.340, L.352, F.353, K.423 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.352 Water bridges: A:G.341 GOL.15: 2 residues within 4Å: Chain A: S.30, A.31 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.31 GOL.16: 2 residues within 4Å: Chain A: R.466 Ligands: PEG.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.466, A:R.466 GOL.33: 4 residues within 4Å: Chain B: K.340, L.352, F.353, K.423 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.352 Water bridges: B:G.341 GOL.34: 2 residues within 4Å: Chain B: S.30, A.31 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.31 GOL.35: 2 residues within 4Å: Chain B: R.466 Ligands: PEG.36 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.466, B:R.466

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.17: 5 residues within 4Å: Chain A: N.465, E.469, I.471, T.491 Ligands: GOL.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.465, A:T.491 PEG.18: 2 residues within 4Å: Chain A: K.354, G.355 No protein-ligand interaction detected (PLIP) PEG.19: 4 residues within 4Å: Chain A: A.232, E.279, Y.280, D.281 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.281, A:D.281, A:D.281 Water bridges: A:A.232, A:D.281 PEG.36: 5 residues within 4Å: Chain B: N.465, E.469, I.471, T.491 Ligands: GOL.35 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.465, B:T.491 PEG.37: 2 residues within 4Å: Chain B: K.354, G.355 No protein-ligand interaction detected (PLIP) PEG.38: 4 residues within 4Å: Chain B: A.232, E.279, Y.280, D.281 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.281, B:D.281 Water bridges: B:A.232, B:D.281

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kamariah, N. et al., Crystallographic and solution studies of NAD(+)- and NADH-bound alkylhydroperoxide reductase subunit F (AhpF) from Escherichia coli provide insight into sequential enzymatic steps. Biochim.Biophys.Acta (2015)

Release Date

2015-07-15

Peptides

Alkyl hydroperoxide reductase subunit F: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Alkyl hydroperoxide reductase subunit F

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