SMTL ID : 3olu.1

X-ray crystal structure of 1-arachidonoyl glycerol bound to the cyclooxygenase channel of R513H murine COX-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 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.28, E.40, N.41 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain B: S.11, P.13, Y.28, E.40, N.41 No protein-ligand interaction detected (PLIP)

2 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.114, N.118, Y.121, R.190, F.194 Chain B: L.212 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:D.213, B:D.213, B:D.213 Hydrophobic interactions: A:R.190 NAG-NAG-MAN.4: 6 residues within 4Å: Chain A: L.212 Chain B: E.114, N.118, Y.121, R.190, F.194 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:D.213 Hydrophobic interactions: B:R.190

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

EDO.5: 6 residues within 4Å: Chain A: A.130, D.131, D.132, C.133, T.135, P.136 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.130 EDO.6: 7 residues within 4Å: Chain A: P.136, M.137, L.145, S.429, R.430, K.433, Y.434 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.434 EDO.7: 1 residues within 4Å: Chain A: K.29 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.29, A:K.29 EDO.8: 8 residues within 4Å: Chain A: E.282, R.285, E.313, A.536, S.540, L.541, N.544, N.545 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.285, A:N.544, A:N.545 Water bridges: A:T.535 EDO.9: 4 residues within 4Å: Chain A: K.225, Y.228, V.235, N.284 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.225, A:K.225, A:N.284 EDO.10: 5 residues within 4Å: Chain A: D.213, R.214, K.217, V.245, E.246 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.214, A:R.214, A:E.246 EDO.11: 10 residues within 4Å: Chain A: H.63, Q.166, L.326, S.327, H.487, A.490, I.491, F.492, V.497 Ligands: 1AG.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.63, A:Q.166, A:I.491, A:F.492 EDO.16: 8 residues within 4Å: Chain B: H.63, Q.166, L.326, S.327, H.487, A.490, I.491, F.492 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.166, B:S.327, B:I.491, B:F.492, B:F.492 EDO.17: 4 residues within 4Å: Chain B: K.225, Y.228, V.235, N.284 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.225, B:K.225, B:N.284 EDO.18: 7 residues within 4Å: Chain B: P.136, M.137, L.145, S.429, R.430, K.433, Y.434 No protein-ligand interaction detected (PLIP) EDO.19: 7 residues within 4Å: Chain A: P.521, S.522, G.526, E.527 Chain B: M.21, K.29, D.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.527, A:E.527 EDO.20: 8 residues within 4Å: Chain B: E.282, R.285, E.313, A.536, S.540, L.541, N.544, N.545 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.282, B:R.285, B:N.544, B:N.545 Water bridges: B:R.285, B:T.535 EDO.21: 4 residues within 4Å: Chain A: L.119, L.198 Chain B: S.117, L.119 1 PLIP interactions: 1 interactions with chain B Water bridges: B:L.119 EDO.22: 6 residues within 4Å: Chain B: D.213, R.214, K.217, Q.244, V.245, E.246 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.213, B:R.214, B:K.217, B:E.246

2 x 1AG: (2S)-2,3-dihydroxypropyl (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate(Non-covalent)

1AG.12: 26 residues within 4Å: Chain A: R.94, F.179, F.183, V.202, V.318, Y.322, V.323, L.326, S.327, Y.329, N.349, I.351, F.355, L.358, Y.359, W.361, F.492, M.496, V.497, G.500, A.501, S.504, L.505, G.507, L.508 Ligands: EDO.11 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:F.179, A:F.179, A:F.183, A:V.202, A:V.318, A:Y.322, A:V.323, A:L.326, A:L.326, A:I.351, A:F.355, A:F.355, A:F.355, A:L.358, A:W.361, A:F.492, A:V.497, A:L.508 Hydrogen bonds: A:R.94, A:R.94, A:Y.329 1AG.23: 23 residues within 4Å: Chain B: R.94, F.179, F.183, V.318, Y.322, V.323, L.326, S.327, Y.329, N.349, I.351, F.355, Y.359, W.361, M.496, V.497, G.500, A.501, F.503, S.504, L.505, G.507, L.508 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.179, B:F.179, B:F.183, B:F.183, B:V.318, B:V.323, B:L.326, B:L.326, B:I.351, B:F.355, B:Y.359, B:W.361, B:V.497, B:L.508, B:L.508 Salt bridges: B:R.94

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

COH.13: 17 residues within 4Å: Chain A: Y.122, A.173, A.176, Q.177, H.181, F.184, K.185, T.186, V.269, N.356, Y.359, H.360, W.361, H.362, L.365, L.382, V.421 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:A.176, A:Q.177, A:Q.177, A:F.184, A:V.269, A:Y.359, A:W.361, A:L.382, A:V.421, A:V.421 Hydrogen bonds: A:T.186, A:T.186, A:N.356 Water bridges: A:H.181, A:F.184 Salt bridges: A:H.188 pi-Stacking: A:H.181 Metal complexes: A:H.362 COH.24: 19 residues within 4Å: Chain B: Y.122, A.173, F.174, A.176, Q.177, H.181, F.184, K.185, T.186, H.188, V.269, N.356, Y.359, H.360, W.361, H.362, L.365, L.382, V.421 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:F.174, B:A.176, B:Q.177, B:Q.177, B:F.184, B:V.269, B:Y.359, B:W.361, B:L.365, B:L.365, B:L.382, B:V.421, B:V.421 Hydrogen bonds: B:Y.122, B:T.186, B:N.356 Water bridges: B:F.184 Salt bridges: B:H.188 pi-Stacking: B:H.181 Metal complexes: B:H.362

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

NAG.14: 5 residues within 4Å: Chain A: Q.380, N.384, S.386, I.387, E.390 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.384, A:E.390 NAG.25: 5 residues within 4Å: Chain B: Q.380, N.384, S.386, I.387, E.390 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.390, B:E.390

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

BOG.15: 8 residues within 4Å: Chain A: E.153, K.154, R.158, R.159, R.412, I.416, E.460, E.464 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:E.153, A:I.416 Hydrogen bonds: A:R.159, A:R.412, A:E.460, A:E.464, A:E.464 Water bridges: A:R.412 Salt bridges: A:R.159, A:R.412

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vecchio, A.J. et al., The structural basis of endocannabinoid oxygenation by cyclooxygenase-2. J.Biol.Chem. (2011)

Release Date

2011-04-13

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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