SMTL ID : 3mdl.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 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: 5 residues within 4Å: Chain A: S.11, P.13, Y.28, E.40, N.41 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain B: Y.28, E.40, N.41 No protein-ligand interaction detected (PLIP) NAG-NAG.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 B, 1 interactions with chain A Hydrophobic interactions: B:R.190 Water bridges: A:D.213

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.114, N.118, Y.121, R.190, F.194 Chain B: L.212 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:D.213 Hydrophobic interactions: A:R.190

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

1AG.5: 21 residues within 4Å: Chain A: V.90, L.91, R.94, F.179, Y.322, V.323, L.326, S.327, Y.329, F.355, L.358, Y.359, W.361, F.492, M.496, V.497, G.500, A.501, S.504, L.505, L.508 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.179, A:Y.322, A:V.323, A:V.323, A:L.326, A:L.326, A:Y.329, A:F.355, A:L.358, A:Y.359, A:Y.359, A:W.361, A:W.361, A:F.492, A:V.497, A:L.508, A:L.508 Hydrogen bonds: A:Y.329, A:A.501 Salt bridges: A:R.94 1AG.13: 22 residues within 4Å: Chain B: V.90, R.94, F.179, F.183, 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, S.504, L.505, G.507, L.508 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.179, B:F.179, B:F.183, B:Y.322, B:V.323, B:L.326, B:I.351, B:F.355, B:Y.359, B:W.361, B:V.497, B:A.501, B:L.508, B:L.508 Salt bridges: B:R.94

5 x AKR: ACRYLIC ACID(Non-covalent)

AKR.6: 4 residues within 4Å: Chain A: S.451, F.452, E.453, K.466 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.452, A:K.466 Hydrogen bonds: A:F.452, A:E.453 AKR.7: 6 residues within 4Å: Chain A: T.211, R.214, K.217, Q.244, V.245, E.246 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.246 Salt bridges: A:R.214, A:K.217 AKR.14: 4 residues within 4Å: Chain B: S.451, F.452, E.453, K.466 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.452, B:K.466 Hydrogen bonds: B:S.451, B:F.452, B:E.453 Water bridges: B:S.451 AKR.15: 7 residues within 4Å: Chain B: T.211, D.213, R.214, K.217, Q.244, V.245, E.246 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.246 Salt bridges: B:R.214, B:K.217 AKR.16: 1 residues within 4Å: Chain B: N.60 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.60 Water bridges: B:N.60

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 7 residues within 4Å: Chain A: H.7, C.9, C.10, P.128, V.129, A.130, C.133 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.7, A:A.130 Water bridges: A:Q.435 GOL.12: 4 residues within 4Å: Chain A: Q.517 Chain B: R.17, R.34, Y.96 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.34, A:Q.517, A:Q.517 Water bridges: B:N.16 GOL.17: 7 residues within 4Å: Chain B: H.7, C.9, C.10, P.128, V.129, A.130, C.133 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.130, B:Q.435 Water bridges: B:H.7, B:G.109, B:Q.435

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

COH.9: 19 residues within 4Å: Chain A: 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 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:F.174, A:A.176, A:Q.177, A:F.184, A:F.184, A:V.269, A:Y.359, A:Y.359, A:W.361, A:L.365, A:L.382, A:V.421, A:V.421 Hydrogen bonds: A:T.186, A:T.186, A:N.356 Water bridges: A:F.184 Salt bridges: A:H.188 pi-Stacking: A:H.181, A:H.360 Metal complexes: A:H.362 COH.18: 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, H.362, L.365, L.382, V.421, Q.428 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:F.184, B:V.269, B:Y.359, B:L.365, B:L.382, B:V.421 Hydrogen bonds: B:Y.122, B:T.186, B:N.356, B:Q.428 Water bridges: B:F.184 Salt bridges: B:H.188, 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.10: 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.19: 4 residues within 4Å: Chain B: Q.380, N.384, S.386, I.387 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.384

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

BOG.11: 9 residues within 4Å: Chain A: E.153, K.154, L.157, R.158, R.159, R.412, I.416, E.460, E.464 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.157, A:I.416 Hydrogen bonds: A:R.159, A:R.412, A:E.460, A:E.464, A:E.464 Salt bridges: A:R.159

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