SMTL ID : 4o5q.1

Crystal Structure of the Alkylhydroperoxide Reductase AhpF from Escherichia coli

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 39 residues within 4Å: Chain A: V.218, G.219, S.220, G.221, P.222, A.223, G.224, G.242, E.243, R.244, G.247, Q.248, I.249, T.252, D.254, I.255, E.256, N.257, Q.288, S.289, A.290, A.321, T.322, G.323, A.324, W.326, Y.344, C.348, N.454, W.457, G.487, D.488, K.495, Q.496, I.497, I.498, A.500 Chain B: Y.230 Ligands: GOL.19 34 PLIP interactions: 33 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.252, A:W.326 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:N.257, A:N.257, A:A.290, A:A.290, A:A.324, A:D.488, A:K.495, A:I.497, B:Y.230 Water bridges: A:G.224, A:E.243, A:R.244, A:R.244, A:R.244, A:Q.248, A:N.257, A:N.257, A:A.324, A:N.454, A:N.454, A:N.454, A:C.489, A:C.489, A:I.498 FAD.26: 39 residues within 4Å: Chain A: Y.230 Chain B: V.218, G.219, S.220, G.221, P.222, A.223, G.224, G.242, E.243, R.244, G.247, Q.248, I.249, T.252, D.254, I.255, E.256, N.257, Q.288, S.289, A.290, A.321, T.322, G.323, A.324, W.326, Y.344, C.348, N.454, W.457, G.487, D.488, K.495, Q.496, I.497, I.498, A.500 Ligands: GOL.44 34 PLIP interactions: 33 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.252, B:W.326 Hydrogen bonds: B:S.220, B:G.221, B:A.223, 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:E.243, B:R.244, B:R.244, B:R.244, B:Q.248, B:N.257, B:N.257, B:A.324, B:N.454, B:N.454, B:N.454, B:D.488, B:C.489, B:C.489, B:I.498

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

SO4.2: 4 residues within 4Å: Chain A: A.105, Q.106, S.107 Ligands: PGE.18 Ligand excluded by PLIP SO4.3: 5 residues within 4Å: Chain A: G.364, N.365, S.366, G.450 Ligands: PGE.21 Ligand excluded by PLIP SO4.4: 5 residues within 4Å: Chain A: P.453, N.454, T.455, N.456, W.457 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: 2 residues within 4Å: Chain A: R.357, H.380 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: H.438, N.439 Ligands: PGE.10 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain A: D.29, S.30, A.31, K.32 Ligand excluded by PLIP SO4.9: 2 residues within 4Å: Chain A: D.473, A.474 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain B: A.105, Q.106, S.107 Ligands: PGE.43 Ligand excluded by PLIP SO4.28: 5 residues within 4Å: Chain B: G.364, N.365, S.366, G.450 Ligands: PGE.46 Ligand excluded by PLIP SO4.29: 5 residues within 4Å: Chain B: P.453, N.454, T.455, N.456, W.457 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain B: P.332, G.333, E.334, D.335, Q.336 Ligand excluded by PLIP SO4.31: 2 residues within 4Å: Chain B: R.357, H.380 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain B: H.438, N.439 Ligands: PGE.35 Ligand excluded by PLIP SO4.33: 4 residues within 4Å: Chain B: D.29, S.30, A.31, K.32 Ligand excluded by PLIP SO4.34: 2 residues within 4Å: Chain B: D.473, A.474 Ligand excluded by PLIP

12 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.10: 4 residues within 4Å: Chain A: N.439, I.440, E.441 Ligands: SO4.7 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.439, A:N.439, A:I.440, A:E.441 PGE.11: 8 residues within 4Å: Chain A: E.463, I.471, I.472, D.473, E.477, T.478, N.479 Ligands: PGE.16 No protein-ligand interaction detected (PLIP) PGE.12: 13 residues within 4Å: Chain A: D.214, I.236, R.316, F.512, L.515, I.516, K.519 Chain B: I.372, D.373, A.375, G.376, K.399, L.403 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.214, A:K.519 Water bridges: A:R.316 PGE.16: 7 residues within 4Å: Chain A: E.477, T.478, N.479, V.480, K.481 Ligands: PGE.11, GOL.25 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.481, A:K.481 PGE.18: 6 residues within 4Å: Chain A: S.102, K.103, E.104, A.105, Q.106 Ligands: SO4.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.104, A:Q.106 Water bridges: A:Q.106 PGE.21: 11 residues within 4Å: Chain A: W.326, R.327, Y.344, S.366, V.447, Q.448, I.449, G.450, L.451, M.467 Ligands: SO4.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.327, A:R.327, A:I.449, A:G.450, A:L.451 Water bridges: A:L.451, A:L.451 PGE.35: 4 residues within 4Å: Chain B: N.439, I.440, E.441 Ligands: SO4.32 4 PLIP interactions: 4 interactions with chain B Water bridges: B:N.439, B:N.439, B:I.440, B:E.441 PGE.36: 8 residues within 4Å: Chain B: E.463, I.471, I.472, D.473, E.477, T.478, N.479 Ligands: PGE.41 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.473 PGE.37: 13 residues within 4Å: Chain A: I.372, D.373, A.375, G.376, K.399, L.403 Chain B: D.214, I.236, R.316, F.512, L.515, I.516, K.519 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.214, B:K.519 Water bridges: B:R.316 PGE.41: 7 residues within 4Å: Chain B: E.477, T.478, N.479, V.480, K.481 Ligands: PGE.36, GOL.50 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.481, B:K.481 PGE.43: 6 residues within 4Å: Chain B: S.102, K.103, E.104, A.105, Q.106 Ligands: SO4.27 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.104, B:Q.106 Water bridges: B:Q.106 PGE.46: 11 residues within 4Å: Chain B: W.326, R.327, Y.344, S.366, V.447, Q.448, I.449, G.450, L.451, M.467 Ligands: SO4.28 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.327, B:R.327, B:I.449, B:G.450, B:L.451 Water bridges: B:L.451, B:L.451

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 10 residues within 4Å: Chain A: W.96, H.100, P.101, S.102, Q.106, L.109, R.113, L.141, V.144, L.145 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.102, A:Q.106, A:R.113 GOL.15: 8 residues within 4Å: Chain A: A.232, R.233, K.234, G.235, Y.280 Chain B: P.351, K.354, I.377 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:K.354 Hydrogen bonds: A:R.233 GOL.19: 9 residues within 4Å: Chain A: T.252, V.253, D.254, T.339, V.342, T.343, Y.344, D.349 Ligands: FAD.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.253, A:D.254, A:T.343 Water bridges: A:T.252, A:D.349 GOL.22: 7 residues within 4Å: Chain A: T.339, K.340, G.341, L.352, F.353, K.423, A.443 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.339, A:K.340 Water bridges: A:G.341, A:V.424 GOL.23: 1 residues within 4Å: Chain A: K.391 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.391 GOL.24: 6 residues within 4Å: Chain A: G.300, R.316, T.518, K.519, T.520, A.521 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.300, A:R.316 GOL.25: 8 residues within 4Å: Chain A: E.299, E.477, K.481, D.513, Y.514, R.517, T.518 Ligands: PGE.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.481, A:R.517 Water bridges: A:D.513 GOL.38: 10 residues within 4Å: Chain B: W.96, H.100, P.101, S.102, Q.106, L.109, R.113, L.141, V.144, L.145 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.102, B:Q.106, B:R.113 GOL.40: 8 residues within 4Å: Chain A: P.351, K.354, I.377 Chain B: A.232, R.233, K.234, G.235, Y.280 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.233 Water bridges: A:K.354 GOL.44: 9 residues within 4Å: Chain B: T.252, V.253, D.254, T.339, V.342, T.343, Y.344, D.349 Ligands: FAD.26 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.253, B:D.254, B:T.343 Water bridges: B:T.252, B:D.349 GOL.47: 7 residues within 4Å: Chain B: T.339, K.340, G.341, L.352, F.353, K.423, A.443 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.339, B:K.340 Water bridges: B:G.341, B:V.424 GOL.48: 1 residues within 4Å: Chain B: K.391 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.391 GOL.49: 6 residues within 4Å: Chain B: G.300, R.316, T.518, K.519, T.520, A.521 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.300, B:R.316 GOL.50: 8 residues within 4Å: Chain B: E.299, E.477, K.481, D.513, Y.514, R.517, T.518 Ligands: PGE.41 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.481, B:R.517 Water bridges: B:E.477, B:D.513

2 x CD: CADMIUM ION(Non-covalent)

CD.14: 3 residues within 4Å: Chain A: E.110, R.113, H.114 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.110, A:E.110, A:H.114, H2O.14 CD.39: 3 residues within 4Å: Chain B: E.110, R.113, H.114 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.110, B:E.110, B:H.114, H2O.33

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.17: 4 residues within 4Å: Chain A: F.245, K.274, V.284, D.286 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.274 PG4.42: 4 residues within 4Å: Chain B: F.245, K.274, V.284, D.286 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.274

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.20: 1 residues within 4Å: Chain A: E.416 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.416 TRS.45: 1 residues within 4Å: Chain B: E.416 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.416

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dip, P.V. et al., Structure, mechanism and ensemble formation of the alkylhydroperoxide reductase subunits AhpC and AhpF from Escherichia coli. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-11-05

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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