SMTL ID : 1igx.1

Crystal Structure of Eicosapentanoic Acid Bound in the Cyclooxygenase Channel of Prostaglandin Endoperoxide H Synthase-1.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NDG.1: 4 residues within 4Å: Chain A: Y.14, P.16, Y.31, N.44 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.31, A:N.44 Hydrophobic interactions: A:Y.14 NAG-NDG.9: 4 residues within 4Å: Chain B: Y.14, P.16, Y.31, N.44 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.44 Hydrophobic interactions: B:Y.14

2 x NAG- NAG- BMA- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA-MAN.2: 9 residues within 4Å: Chain A: E.116, N.120, Y.123, M.192, F.196 Chain B: L.214, Y.218, Q.219, P.246 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:M.192, A:F.196 Water bridges: B:Q.219, B:Q.219 Hydrogen bonds: B:P.246 NAG-NAG-BMA-BMA-MAN.10: 9 residues within 4Å: Chain A: L.214, Y.218, Q.219, P.246 Chain B: E.116, N.120, Y.123, M.192, F.196 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:M.192, B:F.196 Water bridges: A:Q.219, A:Q.219 Hydrogen bonds: A:P.246

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 7 residues within 4Å: Chain A: Y.378, E.381, Q.382, N.386, S.388, M.389, D.392 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.382 NAG-NAG.11: 7 residues within 4Å: Chain B: Y.378, E.381, Q.382, N.386, S.388, M.389, D.392 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.382

4 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.4: 5 residues within 4Å: Chain A: P.60, S.61, S.63, F.64, F.67 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.60, A:F.64 Hydrogen bonds: A:S.61 BOG.6: 2 residues within 4Å: Chain A: R.73, W.74 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.74 BOG.12: 5 residues within 4Å: Chain B: P.60, S.61, S.63, F.64, F.67 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.60, B:F.64 Hydrogen bonds: B:S.61 BOG.14: 2 residues within 4Å: Chain B: R.73, W.74 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.74

2 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.5: 6 residues within 4Å: Chain A: P.62, I.65, V.92, V.95, R.96, E.500 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.62, A:R.96, A:R.96 Salt bridges: A:R.96 BGC.13: 6 residues within 4Å: Chain B: P.62, I.65, V.92, V.95, R.96, E.500 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.62, B:R.96, B:R.96 Salt bridges: B:R.96

2 x COH: PROTOPORPHYRIN IX CONTAINING CO(Non-covalent)

COH.7: 18 residues within 4Å: Chain A: Y.124, Q.179, H.183, F.186, K.187, T.188, L.271, N.358, Y.361, H.362, W.363, H.364, M.367, L.384, I.420, H.422, V.423, D.426 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:Q.179, A:Q.179, A:L.271, A:W.363, A:L.384, A:I.420, A:V.423 Hydrogen bonds: A:Y.124, A:T.188, A:T.188, A:N.358, A:D.426 Salt bridges: A:H.183 pi-Stacking: A:H.183, A:H.183, A:H.364, A:H.364, A:H.364 Metal complexes: A:H.364 COH.15: 18 residues within 4Å: Chain B: Y.124, Q.179, H.183, F.186, K.187, T.188, L.271, N.358, Y.361, H.362, W.363, H.364, M.367, L.384, I.420, H.422, V.423, D.426 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:Q.179, B:Q.179, B:L.271, B:W.363, B:L.384, B:I.420, B:V.423 Hydrogen bonds: B:T.188, B:T.188, B:T.188, B:N.358, B:D.426, B:D.426 Salt bridges: B:H.183 pi-Stacking: B:H.183, B:H.183, B:H.364, B:H.364, B:H.364 Metal complexes: B:H.364

2 x EPA: 5,8,11,14,17-EICOSAPENTAENOIC ACID(Non-covalent)

EPA.8: 21 residues within 4Å: Chain A: V.92, R.96, F.181, F.185, V.320, Y.324, V.325, L.328, S.329, Y.331, F.357, Y.361, W.363, M.498, I.499, G.502, A.503, S.506, L.507, G.509, L.510 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.181, A:F.185, A:V.320, A:Y.324, A:V.325, A:L.328, A:Y.331, A:F.357, A:W.363, A:W.363, A:I.499, A:A.503, A:L.510 Salt bridges: A:R.96 EPA.16: 21 residues within 4Å: Chain B: V.92, R.96, F.181, F.185, V.320, Y.324, V.325, L.328, S.329, Y.331, F.357, Y.361, W.363, M.498, I.499, G.502, A.503, S.506, L.507, G.509, L.510 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.181, B:F.185, B:V.320, B:Y.324, B:V.325, B:L.328, B:Y.331, B:F.357, B:W.363, B:W.363, B:I.499, B:A.503, B:L.510 Hydrogen bonds: B:Y.331 Salt bridges: B:R.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malkowski, M.G. et al., Structure of eicosapentaenoic and linoleic acids in the cyclooxygenase site of prostaglandin endoperoxide H synthase-1. J.Biol.Chem. (2001)

Release Date

2001-12-12

Peptides

Prostaglandin Endoperoxide H Synthase-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Prostaglandin Endoperoxide H Synthase-1

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