SMTL ID : 4ykg.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 32 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, T.252, I.255, N.257, Q.288, S.289, A.290, A.321, T.322, G.323, C.345, C.348, N.454, W.457, G.487, D.488, K.495, Q.496, I.497, A.500 Chain B: Y.230 26 PLIP interactions: 25 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.252 Hydrogen bonds: A:S.220, A:G.221, A:A.223, A:E.243, A:R.244, A:R.244, A:G.247, A:Q.248, 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:E.243, A:E.256, A:E.256, A:G.323, A:N.454, A:C.489, A:I.498, B:Y.230 FAD.21: 32 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, T.252, I.255, N.257, Q.288, S.289, A.290, A.321, T.322, G.323, C.345, C.348, N.454, W.457, G.487, D.488, K.495, Q.496, I.497, A.500 27 PLIP interactions: 26 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.252 Hydrogen bonds: B:S.220, B:G.221, B:A.223, B:E.243, B:E.243, B:R.244, 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:E.243, B:E.256, B:E.256, B:G.323, B:N.454, B:C.489, B:I.498

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 15 residues within 4Å: Chain A: I.361, G.362, G.363, G.364, N.365, S.366, L.384, E.385, F.386, A.387, K.391, I.449, L.451, M.467, P.493 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.451 Hydrogen bonds: A:G.362, A:G.363, A:S.366, A:S.366, A:S.366, A:F.386, A:A.387, A:P.493 Water bridges: A:G.364, A:N.365, A:N.365, A:G.367, A:K.495 Salt bridges: A:K.391 pi-Stacking: A:F.386 NAD.22: 15 residues within 4Å: Chain B: I.361, G.362, G.363, G.364, N.365, S.366, L.384, E.385, F.386, A.387, K.391, I.449, L.451, M.467, P.493 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.451 Hydrogen bonds: B:G.362, B:G.363, B:S.366, B:S.366, B:S.366, B:F.386, B:A.387, B:P.493 Water bridges: B:G.364, B:N.365, B:N.365, B:G.367, B:K.495 Salt bridges: B:K.391 pi-Stacking: B:F.386

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

SO4.3: 5 residues within 4Å: Chain A: P.453, N.454, T.455, N.456, W.457 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain A: H.438, N.439 Ligand excluded by PLIP SO4.5: 5 residues within 4Å: Chain A: P.332, G.333, E.334, D.335, Q.336 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: D.393, Q.394, V.395 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: R.357, E.379, H.380 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Chain A: D.473, A.474 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: R.327, N.328, N.330, L.452 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain A: E.279 Chain B: K.354 Ligands: GOL.15 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain A: E.243, S.289 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: 2 residues within 4Å: Chain B: 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: R.357, E.379, H.380 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain B: D.473, A.474 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain B: R.327, N.328, N.330, L.452 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain A: K.354 Chain B: E.279 Ligands: GOL.35 Ligand excluded by PLIP SO4.31: 2 residues within 4Å: Chain B: E.243, S.289 Ligand excluded by PLIP

2 x CD: CADMIUM ION(Non-covalent)

CD.12: 2 residues within 4Å: Chain A: H.85, H.130 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.85, A:H.130, H2O.5 CD.32: 2 residues within 4Å: Chain B: H.85, H.130 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.85, B:H.130, H2O.11

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 3 residues within 4Å: Chain A: L.352, F.353 Ligands: GOL.18 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.356, A:K.356 GOL.14: 1 residues within 4Å: Chain A: R.466 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.466, A:R.466 Water bridges: A:N.465, A:R.466 GOL.15: 2 residues within 4Å: Chain A: D.281 Ligands: SO4.10 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.281, A:D.281, A:D.281 GOL.16: 2 residues within 4Å: Chain A: Q.413, R.432 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.413, A:R.430 GOL.17: 2 residues within 4Å: Chain A: D.278, Y.280 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.278, A:Y.280 GOL.18: 10 residues within 4Å: Chain A: V.253, T.339, K.340, G.341, V.342, T.343, D.349, L.352, F.353 Ligands: GOL.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.339, A:G.341, A:V.342, A:D.349 GOL.33: 3 residues within 4Å: Chain B: L.352, F.353 Ligands: GOL.38 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.356, B:K.356 GOL.34: 1 residues within 4Å: Chain B: R.466 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.466, B:R.466 Water bridges: B:N.465, B:R.466 GOL.35: 2 residues within 4Å: Chain B: D.281 Ligands: SO4.30 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.281, B:D.281 GOL.36: 2 residues within 4Å: Chain B: Q.413, R.432 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.413, B:R.430 GOL.37: 2 residues within 4Å: Chain B: D.278, Y.280 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.280 GOL.38: 10 residues within 4Å: Chain B: V.253, T.339, K.340, G.341, V.342, T.343, D.349, L.352, F.353 Ligands: GOL.33 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.339, B:G.341, B:V.342, B:T.343, B:D.349

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

PEG.19: 3 residues within 4Å: Chain A: L.2, D.3, T.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.3, A:T.4 PEG.20: 4 residues within 4Å: Chain A: E.206, R.210, D.211, R.237 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.211, A:R.237, A:R.237 PEG.39: 3 residues within 4Å: Chain B: L.2, D.3, T.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.4 PEG.40: 4 residues within 4Å: Chain B: E.206, R.210, D.211, R.237 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.211, B:R.237, B:R.237

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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