SMTL ID : 1cvu.1

CRYSTAL STRUCTURE OF ARACHIDONIC ACID BOUND TO THE CYCLOOXYGENASE ACTIVE SITE OF COX-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

1 x THR- LYS- THR- ALA- THR- ILE- ASN- ALA- SER: PROTEIN (9-MER)(Non-covalent)

THR-LYS-THR-ALA-THR-ILE-ASN-ALA-SER.1: 3 residues within 4Å: Chain B: C.538, N.539, C.544 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.535 Water bridges: B:S.535

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: 5 residues within 4Å: Chain A: S.6, P.8, Y.23, E.35, N.36 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain B: S.6, P.8, Y.23, E.35, N.36 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-MAN-MAN.3: 8 residues within 4Å: Chain A: E.109, N.113, Y.116, R.185, F.189 Chain B: L.207, D.208, Q.239 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:R.185 Hydrogen bonds: B:D.208 NAG-NAG-MAN-MAN.5: 7 residues within 4Å: Chain A: L.207, D.208 Chain B: E.109, N.113, Y.116, R.185, F.189 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.208, B:R.185, A:Q.239 Water bridges: A:D.208

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

NAG.6: 5 residues within 4Å: Chain A: Y.371, Q.375, N.379, I.382, E.385 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.371, A:Q.375, A:N.379, A:E.385 NAG.11: 6 residues within 4Å: Chain B: Y.371, Q.375, N.379, S.381, I.382, E.385 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.371, B:N.379, B:E.385, B:E.385

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

BOG.7: 5 residues within 4Å: Chain A: N.55, T.56, Y.59, I.60, P.483 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.56, A:Y.59, A:I.60 Hydrogen bonds: A:T.53, A:N.55, A:T.56 BOG.8: 5 residues within 4Å: Chain A: E.148, R.153, R.154, I.411, Q.414 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.148, A:Q.414 BOG.9: 12 residues within 4Å: Chain A: A.168, Q.172, F.179, T.181, H.183, N.351, Y.354, H.355, W.356, L.359, L.360, Q.423 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.354, A:L.359, A:L.360 Hydrogen bonds: A:T.181, A:H.183, A:N.351, A:Q.423 Water bridges: A:Q.172, A:T.175 Salt bridges: A:H.355 BOG.12: 5 residues within 4Å: Chain B: N.55, T.56, Y.59, F.64, P.483 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:T.56, B:Y.59, B:Y.59 Hydrogen bonds: B:N.55, B:T.56 BOG.13: 12 residues within 4Å: Chain B: A.168, Q.172, F.179, T.181, H.183, N.351, Y.354, H.355, W.356, L.359, L.360, Q.423 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.359, B:L.360 Hydrogen bonds: B:H.183, B:N.351, B:Q.423 Water bridges: B:Q.172, B:T.175 Salt bridges: B:H.355

2 x ACD: ARACHIDONIC ACID(Non-covalent)

ACD.10: 17 residues within 4Å: Chain A: L.86, F.174, I.314, Y.317, V.318, S.322, Y.324, F.350, Y.354, W.356, F.487, M.491, G.495, A.496, S.499, L.500, L.503 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.86, A:I.314, A:I.314, A:Y.317, A:V.318, A:Y.324, A:F.350, A:W.356, A:F.487, A:A.496, A:L.500 Hydrogen bonds: A:Y.354 ACD.14: 18 residues within 4Å: Chain B: L.86, R.89, F.174, I.314, Y.317, V.318, S.322, Y.324, F.350, Y.354, W.356, F.487, M.491, V.492, G.495, A.496, S.499, L.503 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.314, B:Y.317, B:V.318, B:Y.324, B:F.350, B:W.356, B:F.487, B:V.492, B:A.496 Hydrogen bonds: B:Y.354

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kiefer, J.R. et al., Structural insights into the stereochemistry of the cyclooxygenase reaction. Nature (2000)

Release Date

2000-05-16

Peptides

PROSTAGLANDIN H2 SYNTHASE-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PROSTAGLANDIN H2 SYNTHASE-2