SMTL ID : 3hs7.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

3 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.3: 4 residues within 4Å: Chain B: P.12, 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: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.212, A:D.212 Hydrophobic interactions: B:R.189

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: 6 residues within 4Å: Chain A: E.113, N.117, Y.120, R.189, F.193 Chain B: L.211 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.189 Hydrogen bonds: A:R.189

3 x AKR: ACRYLIC ACID(Non-covalent)

AKR.5: 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:K.465 Hydrogen bonds: A:S.450, A:F.451, A:E.452, A:E.452 AKR.15: 4 residues within 4Å: Chain B: S.450, F.451, E.452, K.465 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.451, B:K.465 Hydrogen bonds: B:F.451, B:E.452 AKR.16: 5 residues within 4Å: Chain B: T.210, R.213, K.216, V.244, E.245 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.245 Salt bridges: B:R.213, B:K.216

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

COH.6: 18 residues within 4Å: Chain A: A.172, A.175, Q.176, H.180, F.183, T.185, H.187, L.267, V.268, N.355, Y.358, H.359, W.360, H.361, L.364, L.381, V.420, Q.427 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:A.175, A:Q.176, A:F.183, A:F.183, A:L.267, A:V.268, A:Y.358, A:W.360, A:L.364, A:L.381 Hydrogen bonds: A:F.183, A:T.185, A:N.355, A:Q.427 Salt bridges: A:H.187 pi-Stacking: A:H.180 Metal complexes: A:H.361 COH.17: 19 residues within 4Å: Chain B: A.172, F.173, A.175, Q.176, T.179, H.180, F.183, K.184, T.185, H.187, V.268, N.355, Y.358, H.359, W.360, H.361, L.364, L.381, V.420 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:F.173, B:A.175, B:Q.176, B:Q.176, B:F.183, B:F.183, B:V.268, B:Y.358, B:Y.358, B:W.360, B:L.364, B:L.364, B:L.381, B:V.420 Hydrogen bonds: B:F.183, B:T.185, B:T.185 Salt bridges: B:H.187, B:H.187 pi-Stacking: B:H.180 Metal complexes: B:H.361

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

NAG.7: 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.18: 5 residues within 4Å: Chain B: Q.379, N.383, S.385, I.386, E.389 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.383, B:E.389

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

BOG.8: 7 residues within 4Å: Chain A: E.152, K.153, R.157, R.158, R.411, E.459, E.463 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:E.152 Hydrogen bonds: A:R.158, A:R.411, A:E.459, A:E.463 Salt bridges: A:R.158, A:R.411 BOG.19: 6 residues within 4Å: Chain B: E.152, L.156, R.157, R.158, I.415, Q.418 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.158, B:I.415 Hydrogen bonds: B:Q.418

2 x HXA: DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID(Non-covalent)

HXA.9: 21 residues within 4Å: Chain A: R.93, F.178, F.182, G.200, Y.321, V.322, L.325, S.326, Y.328, N.348, I.350, F.354, Y.358, W.360, V.496, G.499, A.500, S.503, L.504, G.506, L.507 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.178, A:F.178, A:V.322, A:V.322, A:L.325, A:L.325, A:Y.328, A:I.350, A:F.354, A:F.354, A:Y.358, A:W.360, A:V.496, A:L.507 Hydrogen bonds: A:Y.328 Salt bridges: A:R.93 HXA.20: 23 residues within 4Å: Chain B: V.89, R.93, F.178, F.182, V.317, Y.321, V.322, L.325, S.326, Y.328, N.348, I.350, F.354, Y.358, W.360, M.495, V.496, G.499, A.500, S.503, L.504, G.506, L.507 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.178, B:F.178, B:F.182, B:V.317, B:V.322, B:L.325, B:Y.328, B:I.350, B:F.354, B:F.354, B:Y.358, B:W.360, B:W.360, B:V.496, B:A.500, B:L.507 Hydrogen bonds: B:Y.328 Salt bridges: B:R.93

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

EDO.10: 5 residues within 4Å: Chain A: D.212, R.213, K.216, V.244, E.245 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.212, A:R.213, A:E.245 EDO.11: 9 residues within 4Å: Chain A: H.62, Q.165, L.325, S.326, R.486, A.489, I.490, F.491, V.496 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.62, A:L.325, A:R.486, A:I.490, A:F.491 EDO.12: 4 residues within 4Å: Chain A: K.224, Y.227, V.234, N.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.224, A:K.224, A:N.283 EDO.13: 2 residues within 4Å: Chain A: L.388, E.389 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.388, A:E.389 EDO.14: 7 residues within 4Å: Chain A: P.135, M.136, L.144, S.428, R.429, K.432, Y.433 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.433 EDO.21: 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:S.428, B:R.429 EDO.22: 9 residues within 4Å: Chain B: H.62, Q.165, L.325, S.326, R.486, A.489, I.490, F.491, V.496 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.62, B:R.486, B:I.490, B:F.491 EDO.23: 1 residues within 4Å: Chain B: Q.556 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.556

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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