SMTL ID : 5jvz.1

Crystal structure of flurbiprofen bound to S121P murine COX-2 mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 7 residues within 4Å: Chain A: E.109, N.113, Y.116, R.185, F.189 Chain B: L.207, D.208 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:R.185 Hydrogen bonds: A:R.185, B:D.208

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.2: 6 residues within 4Å: Chain A: L.207 Chain B: E.109, N.113, Y.116, R.185, F.189 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.185 Hydrogen bonds: B:R.185

2 x FLP: FLURBIPROFEN(Non-covalent)

FLP.3: 13 residues within 4Å: Chain A: V.85, R.89, V.318, L.321, Y.324, L.328, Y.354, W.356, V.492, G.495, A.496, S.499, L.500 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.318, A:L.321, A:Y.324, A:L.328, A:Y.354, A:W.356, A:V.492, A:A.496 Hydrogen bonds: A:Y.324, A:Y.324 Salt bridges: A:R.89 FLP.11: 14 residues within 4Å: Chain B: V.85, R.89, V.318, L.321, S.322, Y.324, L.328, Y.354, W.356, M.491, G.495, A.496, S.499, L.500 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.318, B:L.321, B:Y.324, B:L.328, B:W.356, B:A.496 Salt bridges: B:R.89

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

BOG.4: 8 residues within 4Å: Chain A: P.54, V.57, L.61, Y.84, V.85, S.88, R.89, L.92 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.57, A:L.61, A:Y.84, A:V.85 Hydrogen bonds: A:S.88, A:S.88, A:R.89 Salt bridges: A:R.89 BOG.6: 8 residues within 4Å: Chain A: E.148, K.149, R.153, R.154, R.407, I.411, E.455, E.459 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:E.148, A:I.411 Hydrogen bonds: A:K.149, A:K.149, A:R.154, A:R.407, A:R.407, A:E.455, A:E.459, A:E.459 Salt bridges: A:R.154

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

COH.5: 15 residues within 4Å: Chain A: Y.117, A.168, Q.172, H.176, F.179, K.180, T.181, H.183, L.263, N.351, Y.354, H.355, H.357, L.360, V.416 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:Q.172, A:F.179, A:L.263, A:Y.354, A:Y.354, A:L.360, A:L.360, A:V.416 Hydrogen bonds: A:T.181, A:T.181, A:N.351 Salt bridges: A:H.183, A:H.183 pi-Stacking: A:H.176, A:H.355 COH.12: 18 residues within 4Å: Chain B: A.168, A.171, Q.172, T.175, H.176, F.179, K.180, T.181, H.183, V.264, N.351, Y.354, H.355, W.356, H.357, L.360, V.416, Q.423 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:A.171, B:Q.172, B:F.179, B:F.179, B:V.264, B:Y.354, B:W.356, B:L.360, B:V.416 Hydrogen bonds: B:T.181, B:T.181, B:N.351, B:H.355 Salt bridges: B:H.183, B:H.355 pi-Stacking: B:H.176

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

NAG.7: 4 residues within 4Å: Chain A: P.8, Y.23, E.35, N.36 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.35, A:N.36 NAG.8: 6 residues within 4Å: Chain A: Y.371, Q.375, N.379, S.381, I.382, E.385 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.379, A:E.385 NAG.13: 3 residues within 4Å: Chain B: Y.23, E.35, N.36 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.23, B:E.35, B:N.36 Water bridges: B:S.6 NAG.14: 6 residues within 4Å: Chain B: K.374, Q.375, N.379, S.381, I.382, E.385 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.379, B:E.385

4 x AKR: ACRYLIC ACID(Non-covalent)

AKR.9: 5 residues within 4Å: Chain A: T.206, D.208, R.209, V.240, E.241 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.209, A:R.209 Hydrogen bonds: A:E.241 Salt bridges: A:R.209, A:K.212 AKR.10: 6 residues within 4Å: Chain A: S.446, F.447, E.448, A.457, A.458, K.461 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.447, A:E.448, A:K.461 Hydrogen bonds: A:F.447, A:E.448 AKR.16: 5 residues within 4Å: Chain B: T.206, R.209, K.212, V.240, E.241 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:R.209 Hydrogen bonds: B:E.241 Salt bridges: B:R.209, B:K.212 AKR.17: 5 residues within 4Å: Chain B: S.446, F.447, E.448, A.457, K.461 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.447, B:K.461 Hydrogen bonds: B:S.446, B:F.447, B:E.448

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

EDO.15: 4 residues within 4Å: Chain B: K.220, Y.223, V.230, N.279 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.220, B:K.220, B:N.279

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, L. et al., Fatty Acid Binding to the Allosteric Subunit of Cyclooxygenase-2 Relieves a Tonic Inhibition of the Catalytic Subunit. J.Biol.Chem. (2016)

Release Date

2016-10-26

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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