SMTL ID : 5fdq.1

Murine COX-2 S530T mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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.1: 5 residues within 4Å: Chain A: S.10, P.12, Y.27, E.39, N.40 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain A: L.211, D.212 Chain B: E.113, N.117, Y.120, R.189, F.193 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.189, A:D.212 Water bridges: A:L.211

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.2: 7 residues within 4Å: Chain A: E.113, N.117, Y.120, R.189, F.193 Chain B: L.211, D.212 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:R.189 Hydrogen bonds: A:R.189, B:D.212 Water bridges: B:D.212

2 x COH: PROTOPORPHYRIN IX CONTAINING CO(Covalent)

COH.4: 16 residues within 4Å: Chain A: Y.121, A.172, F.173, Q.176, H.180, F.183, K.184, T.185, H.187, N.355, Y.358, H.359, L.364, L.381, V.420, Q.427 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:F.173, A:Q.176, A:F.183, A:F.183, A:Y.358, A:Y.358, A:L.364, A:L.381, A:V.420, A:V.420 Hydrogen bonds: A:T.185, A:T.185, A:N.355, A:Q.427 Water bridges: A:F.183 Salt bridges: A:H.187, A:H.187 pi-Stacking: A:H.180 COH.9: 18 residues within 4Å: Chain B: Y.121, A.172, F.173, A.175, Q.176, H.180, F.183, K.184, T.185, H.187, V.268, N.355, Y.358, H.359, W.360, L.364, V.420, Q.427 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:F.173, B:A.175, B:Q.176, B:F.183, B:F.183, B:V.268, B:Y.358, B:W.360, B:L.364, B:V.420 Hydrogen bonds: B:Y.121, B:T.185, B:N.355, B:Q.427 Water bridges: B:F.183 Salt bridges: B:H.187, B:H.187 pi-Stacking: B:H.180

2 x AKR: ACRYLIC ACID(Non-covalent)

AKR.5: 6 residues within 4Å: Chain A: D.212, R.213, K.216, Q.243, V.244, E.245 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:R.213 Hydrogen bonds: A:D.212, A:E.245 Water bridges: A:R.213 Salt bridges: A:R.213, A:K.216 AKR.10: 4 residues within 4Å: Chain B: R.213, K.216, V.244, E.245 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:R.213 Hydrogen bonds: B:E.245 Salt bridges: B:R.213, B:K.216

2 x 60A: 2-[(2~{R})-2-(hydroxymethyloxy)propoxy]ethanol(Non-covalent)

60A.6: 9 residues within 4Å: Chain A: Y.321, V.322, L.325, S.326, Y.358, W.360, G.499, A.500, T.503 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.360 Hydrogen bonds: A:Y.358, A:Y.358 Water bridges: A:R.93, A:Y.328 60A.11: 11 residues within 4Å: Chain B: Y.321, V.322, S.326, Y.328, Y.358, W.360, M.495, V.496, G.499, A.500, T.503 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.360 Hydrogen bonds: B:Y.328, B:Y.358, B:T.503

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

BOG.7: 7 residues within 4Å: Chain A: E.152, K.153, R.157, R.158, R.411, E.459, E.463 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:E.152 Hydrogen bonds: A:K.153, A:K.153, A:R.158, A:R.411, A:R.411, A:E.459, A:E.463, A:E.463 Salt bridges: A:K.153, A:R.158

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

NAG.8: 4 residues within 4Å: Chain A: Q.379, N.383, S.385, I.386 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.383 NAG.12: 5 residues within 4Å: Chain B: S.10, P.12, Y.27, E.39, N.40 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:E.39 Hydrogen bonds: B:S.10, B:S.10, B:Y.27, B:E.39, B:N.40 Water bridges: B:T.42 NAG.13: 5 residues within 4Å: Chain B: Q.379, N.383, S.385, I.386, E.389 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.383

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lucido, M.J. et al., Crystal Structure of Aspirin-Acetylated Human Cyclooxygenase-2: Insight into the Formation of Products with Reversed Stereochemistry. Biochemistry (2016)

Release Date

2016-03-16

Peptides

Prostaglandin G/H synthase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Prostaglandin G/H synthase 2