SMTL ID : 1u67.1

Crystal Structure of Arachidonic Acid Bound to a Mutant of Prostagladin H Synthase-1 that Forms Predominantly 11-HPETE.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-dimer

Ligands

4 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.38, P.40, Y.55, N.68 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.55, A:N.68 Hydrophobic interactions: A:Y.55 NAG-NDG.3: 7 residues within 4Å: Chain A: Y.402, Q.406, N.410, S.412, M.413, D.416, Y.417 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.410 NAG-NDG.10: 4 residues within 4Å: Chain B: Y.38, P.40, Y.55, N.68 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.68 Hydrophobic interactions: B:Y.55 NAG-NDG.12: 7 residues within 4Å: Chain B: Y.402, Q.406, N.410, S.412, M.413, D.416, Y.417 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.410

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

NAG-NAG-BMA-BMA.2: 9 residues within 4Å: Chain A: E.140, N.144, S.146, Y.147, M.216, F.220 Chain B: L.238, Y.242 Ligands: BOG.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:M.216, A:F.220 NAG-NAG-BMA-BMA.11: 9 residues within 4Å: Chain A: L.238, Y.242 Chain B: E.140, N.144, S.146, Y.147, M.216, F.220 Ligands: BOG.15 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:M.216, B:F.220

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

BOG.4: 3 residues within 4Å: Chain A: S.87, F.88, F.91 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.91 Hydrogen bonds: A:S.87 BOG.5: 10 residues within 4Å: Chain A: P.86, I.89, W.100, L.112, L.115, V.116, V.119, R.120, L.123, E.524 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.100, A:L.112, A:L.115, A:V.116 Hydrogen bonds: A:R.120 Water bridges: A:G.471 Salt bridges: A:R.120 BOG.6: 8 residues within 4Å: Chain A: I.132, A.133, Y.147, F.220 Chain B: Y.242, F.247 Ligands: NAG-NAG-BMA-BMA.2, NAG-NAG-BMA-BMA.2 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.147 Hydrophobic interactions: B:F.247, B:F.247 BOG.7: 4 residues within 4Å: Chain A: G.96, R.97, W.98, L.99 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.98, A:L.99 BOG.13: 3 residues within 4Å: Chain B: S.87, F.88, F.91 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.91 Hydrogen bonds: B:S.87 BOG.14: 10 residues within 4Å: Chain B: P.86, I.89, W.100, L.112, L.115, V.116, V.119, R.120, L.123, E.524 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.100, B:L.112, B:L.115, B:V.116 Hydrogen bonds: B:R.120 Water bridges: B:G.471 Salt bridges: B:R.120 BOG.15: 8 residues within 4Å: Chain A: Y.242, F.247 Chain B: I.132, A.133, Y.147, F.220 Ligands: NAG-NAG-BMA-BMA.11, NAG-NAG-BMA-BMA.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.247, A:F.247 BOG.16: 4 residues within 4Å: Chain B: G.96, R.97, W.98, L.99 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.98, B:L.99

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

COH.8: 19 residues within 4Å: Chain A: Y.148, A.199, Q.203, T.206, H.207, F.210, K.211, T.212, L.295, N.382, Y.385, H.386, F.387, H.388, M.391, I.444, H.446, V.447, D.450 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:Q.203, A:Q.203, A:F.210, A:L.295, A:Y.385, A:F.387, A:I.444 Hydrogen bonds: A:Y.148, A:T.212, A:T.212, A:N.382, A:D.450 pi-Stacking: A:H.207, A:H.207, A:H.386, A:H.388, A:H.388, A:H.388 Metal complexes: A:H.388 COH.17: 19 residues within 4Å: Chain B: Y.148, A.199, Q.203, T.206, H.207, F.210, K.211, T.212, L.295, N.382, Y.385, H.386, F.387, H.388, M.391, I.444, H.446, V.447, D.450 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:Q.203, B:Q.203, B:F.210, B:L.295, B:Y.385, B:F.387, B:I.444 Hydrogen bonds: B:T.212, B:T.212, B:T.212, B:N.382, B:D.450, B:D.450 pi-Stacking: B:H.207, B:H.207, B:H.386, B:H.388, B:H.388, B:H.388 Metal complexes: B:H.388

2 x ACD: ARACHIDONIC ACID(Non-covalent)

ACD.9: 12 residues within 4Å: Chain A: V.116, R.120, A.349, L.352, Y.355, L.359, Y.385, F.387, I.523, G.526, A.527, S.530 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.349, A:L.352, A:Y.355, A:L.359, A:Y.385, A:Y.385, A:F.387, A:I.523, A:A.527 Salt bridges: A:R.120 ACD.18: 12 residues within 4Å: Chain B: V.116, R.120, A.349, L.352, Y.355, L.359, Y.385, F.387, I.523, G.526, A.527, S.530 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.349, B:L.352, B:Y.355, B:L.359, B:Y.385, B:Y.385, B:F.387, B:I.523, B:A.527 Hydrogen bonds: B:Y.355 Salt bridges: B:R.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harman, C.A. et al., Crystal structure of arachidonic Acid bound to a mutant of prostaglandin endoperoxide h synthase-1 that forms predominantly 11-hydroperoxyeicosatetraenoic Acid. J.Biol.Chem. (2004)

Release Date

2004-09-07

Peptides

Prostaglandin G/H synthase 1 precursor: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Prostaglandin G/H synthase 1 precursor