SMTL ID : 1diy.1

CRYSTAL STRUCTURE OF ARACHIDONIC ACID BOUND IN THE CYCLOOXYGENASE ACTIVE SITE OF PGHS-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 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.7, P.9, Y.24, N.37 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.37 Hydrophobic interactions: A:Y.7 NAG-NDG.10: 4 residues within 4Å: Chain B: Y.7, P.9, Y.24, N.37 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.37 Hydrophobic interactions: B:Y.7

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: 10 residues within 4Å: Chain A: E.109, N.113, Y.116, M.185, F.189 Chain B: L.207, E.208, Y.211, Q.212, P.239 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:M.185 Hydrogen bonds: B:E.208, B:P.239 NAG-NAG-BMA-BMA-MAN.11: 10 residues within 4Å: Chain A: L.207, E.208, Y.211, Q.212, P.239 Chain B: E.109, N.113, Y.116, M.185, F.189 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.208, A:E.208, A:P.239 Hydrophobic interactions: B:M.185

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: 5 residues within 4Å: Chain A: Y.371, Q.375, N.379, M.382, D.385 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.371, A:Y.371, A:Q.375 NAG-NAG.12: 5 residues within 4Å: Chain B: Y.371, Q.375, N.379, M.382, D.385 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.371, B:Q.375

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

BOG.4: 4 residues within 4Å: Chain A: S.56, F.57, F.60 Ligands: BOG.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.60 BOG.5: 10 residues within 4Å: Chain A: P.55, I.58, W.69, L.84, V.88, R.89, L.92, G.440, E.493 Ligands: BOG.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.58, A:W.69, A:L.84 Hydrogen bonds: A:V.88 Water bridges: A:G.440 Salt bridges: A:R.89 BOG.6: 4 residues within 4Å: Chain A: I.58, L.84, V.88 Ligands: BOG.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.84 BOG.7: 8 residues within 4Å: Chain A: F.60, L.61, H.64, G.65, W.67, L.68, V.72 Ligands: BOG.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.61, A:L.61, A:L.68, A:V.72 Hydrogen bonds: A:G.65 BOG.13: 4 residues within 4Å: Chain B: S.56, F.57, F.60 Ligands: BOG.16 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.60 BOG.14: 10 residues within 4Å: Chain B: P.55, I.58, W.69, L.84, V.88, R.89, L.92, G.440, E.493 Ligands: BOG.15 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.58, B:W.69, B:L.84 Hydrogen bonds: B:V.88 Water bridges: B:G.440 Salt bridges: B:R.89 BOG.15: 4 residues within 4Å: Chain B: I.58, L.84, V.88 Ligands: BOG.14 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.84 BOG.16: 8 residues within 4Å: Chain B: F.60, L.61, H.64, G.65, W.67, L.68, V.72 Ligands: BOG.13 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.61, B:L.61, B:L.68, B:V.72 Hydrogen bonds: B:G.65

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

COH.8: 18 residues within 4Å: Chain A: Y.117, Q.172, H.176, F.179, K.180, T.181, L.264, N.351, Y.354, H.355, W.356, H.357, M.360, L.377, I.413, H.415, V.416, D.419 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:Q.172, A:L.264, A:W.356, A:L.377, A:I.413, A:V.416 Hydrogen bonds: A:Y.117, A:T.181, A:T.181, A:N.351, A:D.419, A:D.419 pi-Stacking: A:H.176, A:H.357, A:H.357, A:H.357 Metal complexes: A:H.357 COH.17: 18 residues within 4Å: Chain B: Y.117, Q.172, H.176, F.179, K.180, T.181, L.264, N.351, Y.354, H.355, W.356, H.357, M.360, L.377, I.413, H.415, V.416, D.419 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:Q.172, B:L.264, B:W.356, B:L.377, B:I.413, B:V.416 Hydrogen bonds: B:T.181, B:T.181, B:T.181, B:N.351, B:D.419 pi-Stacking: B:H.176, B:H.357, B:H.357, B:H.357 Metal complexes: B:H.357

2 x ACD: ARACHIDONIC ACID(Non-covalent)

ACD.9: 23 residues within 4Å: Chain A: V.85, R.89, F.174, F.178, V.313, Y.317, V.318, L.321, S.322, Y.324, N.344, I.346, F.350, Y.354, W.356, M.491, I.492, G.495, A.496, S.499, L.500, G.502, L.503 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.174, A:F.174, A:F.178, A:F.178, A:V.313, A:Y.317, A:V.318, A:L.321, A:I.346, A:F.350, A:F.350, A:Y.354, A:W.356, A:I.492, A:A.496, A:L.503, A:L.503 Salt bridges: A:R.89 ACD.18: 23 residues within 4Å: Chain B: V.85, R.89, F.174, F.178, V.313, Y.317, V.318, L.321, S.322, Y.324, N.344, I.346, F.350, Y.354, W.356, M.491, I.492, G.495, A.496, S.499, L.500, G.502, L.503 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:F.174, B:F.174, B:F.178, B:F.178, B:V.313, B:Y.317, B:V.318, B:L.321, B:I.346, B:F.350, B:F.350, B:Y.354, B:W.356, B:I.492, B:A.496, B:L.503, B:L.503 Hydrogen bonds: B:Y.324 Salt bridges: B:R.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malkowski, M.G. et al., The productive conformation of arachidonic acid bound to prostaglandin synthase. Science (2000)

Release Date

2000-09-22

Peptides

PROSTAGLANDIN H2 SYNTHASE-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

PROSTAGLANDIN H2 SYNTHASE-1

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