SMTL ID : 3n8w.1

Crystal Structure of R120Q/Native Cyclooxygenase-1 Heterodimer mutant in complex with Flurbiprofen

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG-NDG.1: 4 residues within 4Å: Chain A: Y.7, Y.24, P.36, N.37 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.36, A:Y.7 Hydrogen bonds: A:Y.24 NAG-NDG.4: 3 residues within 4Å: Chain B: Y.7, Y.24, N.37 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.37 Hydrophobic interactions: B:Y.7

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(Non-covalent)

NAG-NAG-BMA.2: 8 residues within 4Å: Chain A: Q.369, Y.371, Q.375, N.379, S.381, M.382, D.385, Y.386 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.375, A:Q.369 Water bridges: A:Y.371, A:Y.371

1 x NAG- NDG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NDG-BMA-MAN-MAN.3: 10 residues within 4Å: Chain A: E.109, N.113, Y.116, M.185, F.189 Chain B: L.207, E.208, Y.211, Q.212, P.239 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:M.185

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.5: 8 residues within 4Å: Chain B: Q.369, Y.371, Q.375, N.379, S.381, M.382, D.385, Y.386 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.369, B:Q.375 Water bridges: B:Y.371, B:Y.386

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

NAG-NDG-BMA.6: 7 residues within 4Å: Chain A: L.207, Y.211 Chain B: E.109, N.113, Y.116, M.185, F.189 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.109, B:Y.116 Water bridges: B:N.113 Hydrophobic interactions: B:M.185

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.7: 18 residues within 4Å: Chain A: A.168, A.171, Q.172, T.175, H.176, F.179, K.180, T.181, L.264, N.351, Y.354, H.355, W.356, H.357, M.360, I.413, V.416, D.419 16 PLIP interactions: 15 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:A.171, A:Q.172, A:Q.172, A:F.179, A:F.179, A:L.264, A:W.356, A:I.413, A:V.416 Hydrogen bonds: A:F.179, A:T.181, A:N.351, A:D.419 pi-Stacking: A:H.176 Metal complexes: A:H.357, H2O.2 HEM.10: 18 residues within 4Å: Chain B: Y.117, A.168, A.171, Q.172, T.175, H.176, F.179, K.180, T.181, L.264, N.351, Y.354, H.355, W.356, H.357, M.360, I.413, V.416 15 PLIP interactions: 14 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:A.171, B:Q.172, B:Q.172, B:F.179, B:F.179, B:L.264, B:W.356, B:I.413, B:V.416 Hydrogen bonds: B:T.181, B:T.181, B:N.351 pi-Stacking: B:H.176 Metal complexes: B:H.357, H2O.6

1 x FLP: FLURBIPROFEN(Non-covalent)

FLP.8: 13 residues within 4Å: Chain A: V.85, R.89, V.318, L.321, Y.324, L.328, Y.354, W.356, M.491, G.495, A.496, S.499, L.500 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.318, A:L.321, A:Y.324, A:L.328, A:W.356, A:W.356, A:A.496, A:L.500 Hydrogen bonds: A:Y.324 Salt bridges: A:R.89

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

BOG.9: 9 residues within 4Å: Chain A: P.55, I.58, L.62, L.84, V.85, V.88, R.89, L.92, E.493 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.58, A:L.62, A:L.84 Hydrogen bonds: A:V.88, A:R.89, A:E.493 Salt bridges: A:R.89 BOG.11: 4 residues within 4Å: Chain B: S.54, S.56, F.57, F.60 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.54, B:S.54 BOG.12: 7 residues within 4Å: Chain B: R.52, P.55, I.58, V.88, Q.89, L.92, E.493 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.52, B:E.493

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sidhu, R.S. et al., Comparison of Cyclooxygenase-1 Crystal Structures: Cross-Talk between Monomers Comprising Cyclooxygenase-1 Homodimers. Biochemistry (2010)

Release Date

2010-07-28

Peptides

Prostaglandin G/H synthase 1: A
Prostaglandin G/H synthase 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Prostaglandin G/H synthase 1

Prostaglandin G/H synthase 1

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