SMTL ID : 3qh0.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

1 x HSQ- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetylamino-2-deoxy-alpha-L-idopyranose(Post Translational Modification)

HSQ-NAG.1: 3 residues within 4Å: Chain A: Y.46, E.58, N.59 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.58 Hydrogen bonds: A:E.58, A:E.58, A:N.59

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 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:D.231, B:D.231, B:D.231 Hydrophobic interactions: A:R.208

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: 4 residues within 4Å: Chain B: P.31, Y.46, E.58, N.59 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.58 Hydrogen bonds: B:E.58, B:N.59

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

NAG-NAG.4: 7 residues within 4Å: Chain A: L.230, D.231 Chain B: E.132, N.136, Y.139, R.208, F.212 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:R.208 Hydrogen bonds: A:D.231 Water bridges: A:D.231

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

EDO.5: 8 residues within 4Å: Chain A: H.81, Q.184, L.344, R.505, A.508, I.509, F.510, V.515 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: P.154, M.155, L.163, S.447, R.448, K.451, Y.452 Ligands: EDO.12 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: C.48, D.49, C.50, F.55 Ligand excluded by PLIP EDO.8: 8 residues within 4Å: Chain A: E.300, R.303, E.331, A.554, S.558, L.559, N.562, N.563 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: K.243, Y.246, V.253, N.302 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: L.238, K.245, Y.246 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: S.135 Chain B: L.137, L.216 Ligands: EDO.13 Ligand excluded by PLIP EDO.12: 8 residues within 4Å: Chain A: V.147, A.148, D.149, C.151, T.153, P.154, K.451 Ligands: EDO.6 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: F.134 Chain B: L.137 Ligands: EDO.11 Ligand excluded by PLIP EDO.20: 9 residues within 4Å: Chain B: H.81, Q.184, L.344, S.345, R.505, A.508, I.509, F.510, V.515 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain B: K.243, Y.246, V.253, N.302, D.306 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain B: P.154, M.155, L.163, S.447, R.448, K.451, Y.452 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain A: P.539, S.540, G.544 Chain B: M.39, D.49 Ligand excluded by PLIP EDO.24: 8 residues within 4Å: Chain B: E.300, R.303, E.331, A.554, S.558, L.559, N.562, N.563 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain A: L.137, L.216 Chain B: S.135, L.137 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain B: D.231, R.232, K.235, Q.262, V.263, E.264 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain B: T.419, R.420, N.573, V.574 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain B: K.167, L.170, Q.437, A.438, K.441 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain B: V.341, S.345, Y.347, V.515, A.519 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain B: Y.377, W.379, M.514, G.518, A.519, S.522 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain B: L.238, K.245, Y.246 Ligand excluded by PLIP EDO.32: 9 residues within 4Å: Chain A: W.131, F.134 Chain B: G.217, H.218, G.219, N.367, G.528, N.529, P.530 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain B: C.561, N.562, N.563, V.564, K.565 Ligand excluded by PLIP

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.14: 14 residues within 4Å: Chain A: V.108, R.112, F.197, Y.340, V.341, S.345, Y.347, Y.377, W.379, V.515, G.518, A.519, S.522, L.523 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.197, A:Y.340, A:V.341, A:V.341, A:W.379, A:V.515, A:A.519 Hydrogen bonds: A:Y.347 Salt bridges: A:R.112

2 x AKR: ACRYLIC ACID(Non-covalent)

AKR.15: 4 residues within 4Å: Chain A: S.469, F.470, E.471, K.484 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.470, A:K.484 Hydrogen bonds: A:F.470, A:E.471 AKR.16: 6 residues within 4Å: Chain A: T.229, R.232, K.235, Q.262, V.263, E.264 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.232, A:E.264 Hydrogen bonds: A:E.264 Salt bridges: A:R.232, A:K.235

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

COH.17: 21 residues within 4Å: Chain A: Y.140, A.191, A.194, Q.195, H.199, F.202, K.203, T.204, H.206, L.286, V.287, N.374, Y.377, H.378, W.379, H.380, L.383, F.387, F.396, L.400, V.439 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:A.194, A:F.202, A:L.286, A:V.287, A:W.379, A:L.383, A:F.387, A:F.396, A:L.400, A:V.439, A:V.439 Hydrogen bonds: A:T.204, A:T.204, A:N.374 Water bridges: A:F.202 Salt bridges: A:H.206, A:H.206 pi-Stacking: A:H.199 COH.34: 19 residues within 4Å: Chain B: Y.140, A.191, F.192, A.194, Q.195, 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 18 PLIP interactions: 18 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:W.379, B:L.383, B:L.400, B:V.439 Hydrogen bonds: B:Y.140, B:T.204, B:N.374, B:N.374 Water bridges: B:Q.446 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.18: 5 residues within 4Å: Chain A: Q.398, N.402, S.404, I.405, E.408 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.408 Water bridges: A:N.402 NAG.35: 5 residues within 4Å: Chain B: Q.398, N.402, S.404, I.405, E.408 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.408 Water bridges: B:Y.394

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

BOG.19: 8 residues within 4Å: Chain A: E.171, K.172, L.175, R.176, R.177, R.430, E.478, E.482 10 PLIP interactions: 10 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 Water bridges: A:E.482 Salt bridges: A:R.177, A:R.430

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, L. et al., Human cyclooxygenase-2 is a sequence homodimer that functions as a conformational heterodimer. 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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