SMTL ID : 1q4g.1

2.0 Angstrom Crystal Structure of Ovine Prostaglandin H2 Synthase-1, in complex with alpha-methyl-4-biphenylacetic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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: P.9, Y.24, P.36, N.37 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.36 Hydrogen bonds: A:Y.24, A:N.37 Water bridges: A:T.39 NAG-NDG.4: 4 residues within 4Å: Chain B: Y.7, P.9, Y.24, N.37 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.37 Hydrophobic interactions: B:Y.7

2 x NAG- NAG- BMA- BMA: beta-D-mannopyranose-(1-6)-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-BMA.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-BMA-BMA.5: 8 residues within 4Å: Chain B: Q.369, Y.371, Q.375, N.379, S.381, M.382, D.385, Y.386 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.371, B:Q.375 Water bridges: B: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(Non-covalent)

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, Y.211, Q.212, P.239 Ligands: GOL.21 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:N.113, A:Y.116, A:Y.116, B:L.207, B:Y.211, B:Y.211 Hydrophobic interactions: A:M.185 Hydrogen bonds: B:Q.212

1 x NAG- NDG- BMA- BMA- BMA: beta-D-mannopyranose-(1-6)-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-BMA.6: 10 residues within 4Å: Chain A: L.207, E.208, Y.211, Q.212, P.239 Chain B: E.109, N.113, Y.116, M.185, F.189 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:L.207, A:Y.211, B:N.113, B:Y.116 Hydrogen bonds: B:Y.116, A:P.239 Hydrophobic interactions: B:M.185

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

BOG.7: 11 residues within 4Å: Chain A: R.52, P.55, I.58, L.62, L.84, V.85, V.88, R.89, L.92, F.439, E.493 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.62, A:L.84, A:V.85 Hydrogen bonds: A:R.89, A:E.493 Water bridges: A:R.52, A:R.52, A:R.89 Salt bridges: A:R.89 BOG.8: 1 residues within 4Å: Chain A: I.43 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.43 BOG.9: 4 residues within 4Å: Chain A: T.39, I.40, P.41, W.46 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.46, A:W.46 Hydrogen bonds: A:T.39 Water bridges: A:T.39 BOG.10: 7 residues within 4Å: Chain A: F.60, L.61, H.64, G.65, W.67, L.68, W.69 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.68 BOG.15: 13 residues within 4Å: Chain B: R.52, P.55, I.58, L.61, L.62, L.84, V.85, V.88, R.89, L.92, F.439, E.493 Ligands: BOG.17 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.61, B:L.62, B:L.84, B:V.85 Hydrogen bonds: B:R.52, B:V.88, B:R.89, B:E.493, B:E.493 Water bridges: B:R.89 Salt bridges: B:R.52, B:R.89 BOG.16: 3 residues within 4Å: Chain B: S.56, F.57, F.60 No protein-ligand interaction detected (PLIP) BOG.17: 6 residues within 4Å: Chain B: R.52, I.58, L.84, T.87, V.88 Ligands: BOG.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.52 BOG.18: 6 residues within 4Å: Chain B: F.60, L.61, H.64, W.67, L.68, W.69 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.61, B:L.68 Water bridges: B:G.65

2 x BFL: 2-(1,1'-BIPHENYL-4-YL)PROPANOIC ACID(Non-covalent)

BFL.11: 14 residues within 4Å: Chain A: V.85, R.89, V.318, L.321, Y.324, L.328, Y.354, W.356, M.491, I.492, 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:I.492, A:A.496 Hydrogen bonds: A:Y.324 Salt bridges: A:R.89 BFL.19: 13 residues within 4Å: Chain B: 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 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.318, B:L.321, B:Y.324, B:L.328, B:Y.354, B:W.356, B:W.356, B:A.496 Salt bridges: B:R.89

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

HEM.12: 21 residues within 4Å: Chain A: 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, Y.373, I.413, V.416, D.419 Ligands: GOL.14 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:A.171, A:Q.172, A:F.179, A:F.179, A:L.264, A:W.356, A:Y.373, A:I.413 Hydrogen bonds: A:Y.117, A:T.181, A:N.351, A:D.419, A:D.419 Water bridges: A:F.179 pi-Stacking: A:H.176, A:H.355 Metal complexes: A:H.357 HEM.20: 23 residues within 4Å: Chain B: Y.117, A.168, A.171, Q.172, T.175, H.176, F.179, K.180, T.181, L.263, L.264, N.351, Y.354, H.355, W.356, H.357, M.360, Y.373, I.413, V.416, D.419, E.423 Ligands: GOL.23 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:A.171, B:Q.172, B:F.179, B:F.179, B:L.263, B:L.264, B:W.356, B:M.360, B:Y.373, B:I.413, B:V.416 Hydrogen bonds: B:Y.117, B:F.179, B:T.181, B:T.181, B:N.351, B:D.419 pi-Stacking: B:H.176, B:H.355 Metal complexes: B:H.357

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 5 residues within 4Å: Chain A: K.220, Y.223, V.230, N.279, D.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.220, A:K.220, A:N.279 GOL.14: 5 residues within 4Å: Chain A: Q.172, H.176, V.260, L.263 Ligands: HEM.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.172 GOL.21: 9 residues within 4Å: Chain A: W.108 Chain B: Y.203, G.204, D.205, N.206, L.207, Q.210, R.302 Ligands: NAG-NDG-BMA-MAN-MAN.3 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.203, B:L.207, B:R.302, B:R.302 Water bridges: B:D.198, B:G.204 GOL.22: 4 residues within 4Å: Chain B: K.220, Y.223, V.230, N.279 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.220, B:N.279 GOL.23: 5 residues within 4Å: Chain B: Q.172, H.176, V.260, L.263 Ligands: HEM.20 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.172

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gupta, K. et al., The 2.0A Resolution Crystal Structure of Prostaglandin H(2) Synthase-1: Structural Insights into an Unusual Peroxidase. J.Mol.Biol. (2004)

Release Date

2004-01-06

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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