SMTL ID : 3hs6.1

X-ray crystal structure of eicosapentaenoic acid bound to the cyclooxygenase channel of cyclooxygenase-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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.1: 3 residues within 4Å: Chain A: Y.27, E.39, N.40 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain A: L.211, D.212 Chain B: E.113, N.117, Y.120, R.189, F.193 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:R.189 Hydrogen bonds: A:D.212 Water bridges: A:D.212

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

NAG-NAG-MAN.2: 7 residues within 4Å: Chain A: E.113, N.117, Y.120, R.189, F.193 Chain B: L.211, D.212 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.189

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

NAG-NDG.3: 3 residues within 4Å: Chain B: Y.27, E.39, N.40 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.39 Hydrogen bonds: B:Y.27, B:E.39, B:N.40

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

EPA.5: 16 residues within 4Å: Chain A: V.89, F.178, Y.321, V.322, S.326, Y.328, Y.358, W.360, F.491, M.495, V.496, G.499, A.500, S.503, L.504, L.507 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.89, A:Y.321, A:V.322, A:Y.358, A:W.360, A:W.360, A:F.491, A:F.491, A:V.496, A:L.504 Hydrogen bonds: A:Y.358, A:Y.358 EPA.16: 22 residues within 4Å: Chain B: F.178, F.182, G.200, V.317, Y.321, V.322, L.325, S.326, Y.328, N.348, I.350, F.354, Y.358, W.360, F.491, M.495, V.496, G.499, A.500, S.503, G.506, L.507 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.178, B:F.182, B:F.182, B:V.317, B:Y.321, B:V.322, B:L.325, B:I.350, B:F.354, B:F.354, B:F.354, B:W.360, B:F.491, B:V.496, B:L.507, B:L.507 Hydrogen bonds: B:Y.328 Salt bridges: B:R.93

4 x AKR: ACRYLIC ACID(Non-covalent)

AKR.6: 4 residues within 4Å: Chain A: S.450, F.451, E.452, K.465 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.451, A:K.465 Hydrogen bonds: A:S.450, A:F.451, A:E.452 AKR.7: 6 residues within 4Å: Chain A: T.210, R.213, K.216, Q.243, V.244, E.245 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.213, A:R.213 Hydrogen bonds: A:E.245 Salt bridges: A:R.213, A:K.216 AKR.17: 4 residues within 4Å: Chain B: S.450, F.451, E.452, K.465 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.465 Hydrogen bonds: B:F.451, B:E.452 AKR.18: 5 residues within 4Å: Chain B: R.213, K.216, Q.243, V.244, E.245 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.245 Hydrogen bonds: B:E.245 Salt bridges: B:R.213, B:K.216

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

COH.8: 16 residues within 4Å: Chain A: A.172, A.175, Q.176, T.179, H.180, F.183, K.184, T.185, H.187, V.268, N.355, Y.358, H.359, H.361, L.364, V.420 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:A.175, A:Q.176, A:F.183, A:F.183, A:V.268, A:L.364, A:V.420, A:V.420 Hydrogen bonds: A:F.183, A:T.185, A:T.185, A:N.355 Salt bridges: A:H.187, A:H.187 pi-Stacking: A:H.180, A:H.359 Metal complexes: A:H.361 COH.19: 18 residues within 4Å: Chain B: Y.121, A.172, F.173, A.175, Q.176, H.180, F.183, K.184, T.185, V.268, N.355, Y.358, H.359, H.361, L.364, L.381, V.420, Q.427 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:F.173, B:A.175, B:Q.176, B:F.183, B:V.268, B:Y.358, B:L.364, B:L.381, B:V.420, B:V.420 Hydrogen bonds: B:Y.121, B:T.185, B:N.355, B:Q.427 Salt bridges: B:H.187 pi-Stacking: B:H.180, B:H.359 Metal complexes: B:H.361

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

NAG.9: 5 residues within 4Å: Chain A: Q.379, N.383, S.385, I.386, E.389 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.383, A:E.389 NAG.20: 5 residues within 4Å: Chain B: Q.379, N.383, S.385, I.386, E.389 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.383, B:E.389, B:E.389

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

BOG.10: 8 residues within 4Å: Chain A: E.152, K.153, L.156, R.157, R.158, R.411, E.459, E.463 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:E.152, A:L.156 Hydrogen bonds: A:R.158, A:R.411, A:E.459, A:E.463, A:E.463 Salt bridges: A:R.158, A:R.411 BOG.21: 7 residues within 4Å: Chain B: K.148, E.152, L.156, R.157, R.158, I.415, Q.418 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.418

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 8 residues within 4Å: Chain A: H.62, Q.165, L.325, R.486, A.489, I.490, F.491, V.496 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.486, A:I.490, A:F.491 EDO.12: 8 residues within 4Å: Chain A: P.135, M.136, L.144, S.428, R.429, K.432, Y.433 Ligands: EDO.13 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.433 EDO.13: 8 residues within 4Å: Chain A: V.128, A.129, D.130, C.132, T.134, P.135, K.432 Ligands: EDO.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.132 EDO.14: 2 residues within 4Å: Chain A: D.30, C.31 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.30, A:D.30, A:C.31 EDO.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.22: 8 residues within 4Å: Chain B: H.62, Q.165, L.325, R.486, A.489, I.490, F.491, V.496 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.325, B:R.486, B:I.490, B:F.491 EDO.23: 4 residues within 4Å: Chain B: K.224, Y.227, V.234, N.283 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.224, B:K.224, B:N.283 EDO.24: 7 residues within 4Å: Chain B: P.135, M.136, L.144, S.428, R.429, K.432, Y.433 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Y.433, B:E.475

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vecchio, A.J. et al., Structural basis of fatty acid substrate binding to cyclooxygenase-2. J.Biol.Chem. (2010)

Release Date

2010-05-12

Peptides

Prostaglandin G/H synthase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Prostaglandin G/H synthase 2

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