SMTL ID : 4e1g.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 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.46, E.58, N.59 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: P.31, Y.46, E.58, N.59 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain A: L.230 Chain B: E.132, N.136, Y.139, R.208, F.212 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:R.208 Water bridges: A:D.231

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.132, N.136, Y.139, R.208, F.212 Chain B: L.230 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:R.208 Water bridges: B:D.231

2 x LNL: ALPHA-LINOLENIC ACID(Non-covalent)

LNL.5: 18 residues within 4Å: Chain A: R.112, F.197, F.201, Y.340, V.341, L.344, S.345, Y.347, N.367, I.369, F.373, Y.377, G.518, A.519, F.521, S.522, G.525, L.526 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.197, A:F.197, A:F.201, A:V.341, A:V.341, A:L.344, A:Y.347, A:I.369, A:F.373, A:F.373, A:Y.377, A:A.519, A:L.526 Hydrogen bonds: A:Y.347, A:Y.347 Salt bridges: A:R.112 LNL.13: 19 residues within 4Å: Chain B: R.112, F.197, F.201, V.336, Y.340, V.341, Y.347, N.367, I.369, F.373, Y.377, M.514, V.515, G.518, A.519, F.521, S.522, G.525, L.526 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.197, B:F.197, B:F.201, B:F.201, B:V.336, B:Y.340, B:V.341, B:V.341, B:I.369, B:F.373, B:F.373, B:Y.377, B:V.515, B:L.526 Salt bridges: B:R.112

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

COH.6: 17 residues within 4Å: Chain A: Y.140, A.191, A.194, Q.195, H.199, F.202, K.203, T.204, H.206, V.287, N.374, Y.377, H.378, W.379, L.383, L.400, V.439 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:A.194, A:Q.195, A:Q.195, A:F.202, A:V.287, A:Y.377, A:Y.377, A:W.379, A:L.400, A:V.439, A:V.439 Hydrogen bonds: A:T.204, A:T.204, A:N.374, A:N.374 Salt bridges: A:H.206 pi-Stacking: A:H.199, A:H.378 COH.14: 20 residues within 4Å: Chain B: Y.140, A.191, F.192, A.194, Q.195, T.198, H.199, F.202, K.203, T.204, H.206, V.287, N.374, Y.377, H.378, W.379, H.380, L.383, L.400, V.439 23 PLIP interactions: 23 interactions with chain B, Hydrophobic interactions: B:F.192, B:A.194, B:Q.195, B:F.202, B:V.287, B:Y.377, B:Y.377, B:W.379, B:L.383, B:L.383, B:L.400, B:V.439, B:V.439 Hydrogen bonds: B:Y.140, B:T.204, B:N.374 Water bridges: B:H.199, B:F.202, B:T.204, B:T.204 Salt bridges: B:H.206 pi-Stacking: B:H.199 Metal complexes: B:H.380

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

NAG.7: 5 residues within 4Å: Chain A: Q.398, N.402, S.404, I.405, E.408 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.402 NAG.15: 5 residues within 4Å: Chain B: Y.394, Q.398, N.402, S.404, I.405 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.402

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

BOG.8: 8 residues within 4Å: Chain A: E.171, K.172, L.175, R.176, R.177, R.430, E.478, E.482 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.171, A:L.175 Hydrogen bonds: A:R.177, A:R.430, A:E.478, A:E.482, A:E.482 Salt bridges: A:R.177

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

EDO.9: 7 residues within 4Å: Chain A: P.154, M.155, L.163, S.447, R.448, K.451, Y.452 No protein-ligand interaction detected (PLIP) EDO.10: 8 residues within 4Å: Chain A: E.300, R.303, E.331, A.554, S.558, L.559, N.562, N.563 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.303, A:S.558, A:N.562, A:N.563 Water bridges: A:T.553 EDO.16: 6 residues within 4Å: Chain B: P.154, L.163, S.447, R.448, K.451, Y.452 No protein-ligand interaction detected (PLIP) EDO.17: 5 residues within 4Å: Chain B: R.232, K.235, Q.262, V.263, E.264 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.232, B:K.235, B:Q.262, B:E.264 EDO.18: 4 residues within 4Å: Chain B: K.243, Y.246, V.253, N.302 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.243, B:K.243, B:N.302 EDO.19: 4 residues within 4Å: Chain A: L.137, L.216 Chain B: S.135, L.137 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.228 EDO.20: 8 residues within 4Å: Chain B: E.300, R.303, E.331, A.554, S.558, L.559, N.562, N.563 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.303, B:S.558, B:N.562, B:N.563 Water bridges: B:T.553

2 x AKR: ACRYLIC ACID(Non-covalent)

AKR.11: 4 residues within 4Å: Chain A: S.469, F.470, E.471, K.484 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.470, A:K.484 Hydrogen bonds: A:F.470, A:E.471 Water bridges: A:E.471 AKR.12: 7 residues within 4Å: Chain A: T.229, D.231, R.232, K.235, Q.262, V.263, E.264 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.232, A:R.232 Hydrogen bonds: A:E.264 Salt bridges: A:R.232, A:K.235

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vecchio, A.J. et al., Investigating Substrate Promiscuity in Cyclooxygenase-2: THE ROLE OF ARG-120 AND RESIDUES LINING THE HYDROPHOBIC GROOVE. J.Biol.Chem. (2012)

Release Date

2012-04-25

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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