SMTL ID : 3n8v.1

Crystal Structure of Unoccupied Cyclooxygenase-1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.05 Å

Oligo State

homo-dimer

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, P.9, Y.24, N.37 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.37 Hydrophobic interactions: A:Y.7 NAG-NDG.4: 4 residues within 4Å: Chain B: P.9, Y.24, P.36, N.37 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.36, B:Y.24 Hydrogen bonds: B:Y.24

2 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: 7 residues within 4Å: Chain A: Q.369, Y.371, Q.375, N.379, M.382, D.385, Y.386 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.375 NAG-NAG.5: 7 residues within 4Å: Chain B: Q.369, Y.371, Q.375, N.379, M.382, D.385, Y.386 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.369, B:Q.369, B:Y.371 Water bridges: B:Q.375, B:Q.375, B:S.381

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(Non-covalent)

NAG-NDG-BMA-MAN-MAN.3: 6 residues within 4Å: Chain A: N.113, Y.116, M.185, F.189 Chain B: L.207, Y.211 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.116 Hydrophobic interactions: A:M.185 Water bridges: B:Q.212

1 x NAG- NDG- BMA- BMA: beta-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

NAG-NDG-BMA-BMA.6: 10 residues within 4Å: Chain A: L.207, E.208, Y.211, Q.212 Chain B: E.109, N.113, S.115, Y.116, M.185, F.189 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.115 Hydrophobic interactions: B:M.185, B:F.189

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

HEM.7: 17 residues within 4Å: Chain A: Y.117, A.168, A.171, Q.172, 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 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:Q.172, A:F.179, A:F.179, A:L.264, A:W.356, A:I.413, A:I.413 Hydrogen bonds: A:T.181, A:T.181, A:N.351 pi-Cation interactions: A:H.176, A:H.355 HEM.11: 19 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, D.419 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:A.171, B:Q.172, B:T.175, B:F.179, B:F.179, B:L.264, B:Y.354, B:I.413, B:V.416, B:V.416 Hydrogen bonds: B:Y.117, B:T.181, B:N.351, B:N.351, B:D.419 pi-Stacking: B:H.176, B:H.355

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

BOG.8: 10 residues within 4Å: Chain A: R.52, P.55, I.58, L.81, L.84, V.85, V.88, R.89, L.92, E.493 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.84, A:V.85 Hydrogen bonds: A:R.52, A:R.52, A:R.89 Salt bridges: A:R.89 BOG.9: 4 residues within 4Å: Chain A: R.66, G.323, Y.324, F.325 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.66, A:R.66 Salt bridges: A:R.66 BOG.12: 3 residues within 4Å: Chain B: S.56, F.57, F.60 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.57, B:F.60 BOG.13: 12 residues within 4Å: Chain B: R.52, P.55, I.58, L.61, W.69, L.81, L.84, V.85, V.88, R.89, L.92, E.493 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.58, B:L.61, B:W.69, B:L.81, B:L.84, B:V.85 Hydrogen bonds: B:R.52, B:V.88, B:R.89, B:R.89, B:E.493 Salt bridges: B:R.89 BOG.14: 2 residues within 4Å: Chain B: R.48, N.91 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 4 residues within 4Å: Chain B: V.318, L.321, G.495, A.496 No protein-ligand interaction detected (PLIP)

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Prostaglandin G/H synthase 1

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