SMTL ID : 5f1a.1

The Crystal Structure of Salicylate Bound to Human Cyclooxygenase-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG-MAN-MAN.1: 7 residues within 4Å: Chain A: E.109, N.113, Y.116, R.185, F.189 Chain B: L.207, R.211 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:R.185 Hydrogen bonds: A:R.185, B:R.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: 8 residues within 4Å: Chain A: L.207, A.208, R.211 Chain B: E.109, N.113, Y.116, R.185, F.189 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:R.185 Hydrogen bonds: B:R.185, A:R.211

2 x SAL: 2-HYDROXYBENZOIC ACID(Non-covalent)

SAL.3: 10 residues within 4Å: Chain A: V.318, L.321, L.353, Y.354, W.356, M.491, G.495, A.496, S.499 Ligands: EDO.8 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.353, A:Y.354, A:W.356, A:W.356 Hydrogen bonds: A:Y.354, A:S.499 SAL.10: 8 residues within 4Å: Chain B: V.318, L.353, Y.354, W.356, M.491, G.495, A.496, S.499 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.353, B:Y.354, B:W.356, B:W.356 Hydrogen bonds: B:S.499, B:S.499

2 x COH: PROTOPORPHYRIN IX CONTAINING CO(Covalent)

COH.4: 19 residues within 4Å: Chain A: Y.117, A.168, A.171, Q.172, H.176, F.179, K.180, T.181, H.183, L.263, V.264, N.351, Y.354, H.355, W.356, L.359, L.360, V.416, Q.423 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:A.171, A:Q.172, A:F.179, A:F.179, A:L.263, A:V.264, A:W.356, A:L.359, A:L.360, A:V.416, A:V.416 Hydrogen bonds: A:T.181, A:N.351, A:Q.423 Salt bridges: A:H.183, A:H.183, A:H.355 pi-Stacking: A:H.176 COH.11: 17 residues within 4Å: Chain B: Y.117, A.168, F.169, Q.172, H.176, F.179, K.180, T.181, H.183, V.264, N.351, Y.354, H.355, L.360, I.377, V.416, Q.423 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:F.169, B:Q.172, B:F.179, B:F.179, B:V.264, B:Y.354, B:L.360, B:I.377, B:V.416 Hydrogen bonds: B:Y.117, B:T.181, B:N.351, B:Q.423 Salt bridges: B:H.183, B:H.183 pi-Stacking: B:H.176

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

NAG.5: 5 residues within 4Å: Chain A: Q.375, N.379, S.381, I.382, E.385 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.375 Hydrogen bonds: A:E.385 Water bridges: A:N.379, A:N.379 NAG.12: 3 residues within 4Å: Chain B: Y.23, E.35, N.36 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.23, B:E.35, B:N.36 NAG.13: 5 residues within 4Å: Chain B: Y.371, Q.375, I.377, N.379, I.382 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.375

3 x AKR: ACRYLIC ACID(Non-covalent)

AKR.6: 5 residues within 4Å: Chain A: R.209, K.212, Q.239, A.240, E.241 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.212 Hydrogen bonds: A:Q.239, A:E.241 Salt bridges: A:R.209, A:K.212 AKR.15: 5 residues within 4Å: Chain B: R.209, K.212, Q.239, A.240, E.241 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.212 Hydrogen bonds: B:E.241 Salt bridges: B:R.209, B:K.212 AKR.16: 4 residues within 4Å: Chain B: N.372, Y.373, Q.374, A.412 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:N.372, B:Y.373, B:Q.374 Hydrogen bonds: B:Y.373

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 9 residues within 4Å: Chain A: E.277, R.280, E.308, I.527, A.531, S.535, L.536, N.539, N.540 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.280, A:I.527, A:S.535, A:S.535, A:N.539, A:N.540 EDO.8: 6 residues within 4Å: Chain A: V.85, R.89, S.322, Y.324, A.496 Ligands: SAL.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.89, A:R.89 EDO.9: 7 residues within 4Å: Chain A: F.178, N.344, I.346, F.350, S.499, G.502, L.503 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.344, A:S.499 Water bridges: A:G.502 EDO.17: 9 residues within 4Å: Chain B: E.277, R.280, E.308, I.527, T.530, A.531, S.535, L.536, N.539 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.277, B:T.530, B:T.530, B:N.539 Water bridges: B:S.535 EDO.18: 7 residues within 4Å: Chain B: F.174, F.178, F.350, F.498, S.499, G.502, L.503 4 PLIP interactions: 4 interactions with chain B Water bridges: B:N.344, B:S.499, B:S.499, B:G.502

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

BOG.14: 6 residues within 4Å: Chain B: E.148, K.149, R.154, R.407, E.455, E.459 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:E.148, B:K.149, B:R.154 Hydrogen bonds: B:R.407, B:R.407, B:E.455, B:E.459 Salt bridges: B:R.154, B:R.407

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