SMTL ID : 1diy.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

10 x NAG: N-ACETYL-D-GLUCOSAMINE(Post Translational Modification)(Non-covalent)

NAG.1: 4 residues within 4Å: Chain A: P.9, Y.24, N.37 Ligands: NDG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.37 NAG.3: 6 residues within 4Å: Chain A: E.109, N.113, Y.116, F.189 Chain B: L.207 Ligands: NAG.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.115, A:S.115 NAG.4: 6 residues within 4Å: Chain A: M.185 Chain B: L.207, E.208, Y.211 Ligands: NAG.3, BMA.5 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:M.185 Hydrogen bonds: B:E.208 NAG.8: 6 residues within 4Å: Chain A: Y.371, Q.375, N.379, M.382, D.385 Ligands: NAG.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.379 NAG.9: 3 residues within 4Å: Chain A: Y.371, Q.375 Ligands: NAG.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.371, A:Y.371, A:Q.375 NAG.16: 4 residues within 4Å: Chain B: P.9, Y.24, N.37 Ligands: NDG.17 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.37 NAG.18: 6 residues within 4Å: Chain A: L.207 Chain B: E.109, N.113, Y.116, F.189 Ligands: NAG.19 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.109, B:S.115, B:S.115, B:Y.116 NAG.19: 6 residues within 4Å: Chain A: L.207, E.208, Y.211 Chain B: M.185 Ligands: NAG.18, BMA.20 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.208, A:E.208 Hydrophobic interactions: B:M.185 NAG.23: 6 residues within 4Å: Chain B: Y.371, Q.375, N.379, M.382, D.385 Ligands: NAG.24 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.379 NAG.24: 3 residues within 4Å: Chain B: Y.371, Q.375 Ligands: NAG.23 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.371, B:Q.375

2 x NDG: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE(Non-covalent)

NDG.2: 2 residues within 4Å: Chain A: Y.7 Ligands: NAG.1 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.7 NDG.17: 2 residues within 4Å: Chain B: Y.7 Ligands: NAG.16 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.7

4 x BMA: BETA-D-MANNOSE(Non-functional Binders)

BMA.5: 2 residues within 4Å: Ligands: NAG.4, BMA.6 No protein-ligand interaction detected (PLIP) BMA.6: 2 residues within 4Å: Ligands: BMA.5, MAN.7 No protein-ligand interaction detected (PLIP) BMA.20: 2 residues within 4Å: Ligands: NAG.19, BMA.21 No protein-ligand interaction detected (PLIP) BMA.21: 2 residues within 4Å: Ligands: BMA.20, MAN.22 No protein-ligand interaction detected (PLIP)

2 x MAN: ALPHA-D-MANNOSE(Non-covalent)

MAN.7: 3 residues within 4Å: Chain B: Q.212, P.239 Ligands: BMA.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.239 MAN.22: 3 residues within 4Å: Chain A: Q.212, P.239 Ligands: BMA.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.239

8 x BOG: B-OCTYLGLUCOSIDE(Non-covalent)

BOG.10: 4 residues within 4Å: Chain A: S.56, F.57, F.60 Ligands: BOG.13 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.60 BOG.11: 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.12 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.58, A:W.69, A:L.84 Hydrogen bonds: A:V.88 Salt bridges: A:R.89 Water bridges: A:G.440 BOG.12: 4 residues within 4Å: Chain A: I.58, L.84, V.88 Ligands: BOG.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.84 BOG.13: 8 residues within 4Å: Chain A: F.60, L.61, H.64, G.65, W.67, L.68, V.72 Ligands: BOG.10 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.25: 4 residues within 4Å: Chain B: S.56, F.57, F.60 Ligands: BOG.28 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.60 BOG.26: 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.27 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.58, B:W.69, B:L.84 Hydrogen bonds: B:V.88 Salt bridges: B:R.89 Water bridges: B:G.440 BOG.27: 4 residues within 4Å: Chain B: I.58, L.84, V.88 Ligands: BOG.26 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.84 BOG.28: 8 residues within 4Å: Chain B: F.60, L.61, H.64, G.65, W.67, L.68, V.72 Ligands: BOG.25 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.14: 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 Metal complexes: A:H.357 pi-Stacking: A:H.176, A:H.357, A:H.357, A:H.357 COH.29: 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 Metal complexes: B:H.357 pi-Stacking: B:H.176, B:H.357, B:H.357, B:H.357

2 x ACD: ARACHIDONIC ACID(Non-covalent)

ACD.15: 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.30: 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   PDBsum   PDBe   CATH   PLIP

Citation

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

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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