SMTL ID : 5f19.1

The Crystal Structure of Aspirin Acetylated Human Cyclooxygenase-2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-dimer

Ligands

2 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.1: 7 residues within 4Å: Chain A: E.109, N.113, Y.116, R.185, F.189 Chain B: L.207, R.211 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:R.211 Hydrophobic interactions: A:R.185, A:F.189 Hydrogen bonds: A:R.185, B:R.211 NAG-NAG-MAN.2: 4 residues within 4Å: Chain B: S.6, P.8, Y.23, N.36 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.3: 8 residues within 4Å: Chain A: L.207, A.208, R.211 Chain B: E.109, N.113, Y.116, R.185, F.189 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.211, B:R.185 Water bridges: A:A.208 Hydrophobic interactions: B:R.185, B:F.189

2 x COH: PROTOPORPHYRIN IX CONTAINING CO(Covalent)

COH.4: 18 residues within 4Å: Chain A: Y.117, A.168, F.169, A.171, Q.172, H.176, F.179, K.180, T.181, H.183, V.264, N.351, Y.354, H.355, H.357, L.360, V.416, Q.423 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:F.169, A:A.171, A:Q.172, A:F.179, A:F.179, A:V.264, A:V.264, A:L.360, A:L.360, 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, A:H.355 Metal complexes: A:H.357 COH.16: 14 residues within 4Å: Chain B: Y.117, A.168, Q.172, H.176, F.179, K.180, T.181, H.183, N.351, Y.354, H.355, H.357, L.360, F.364 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:Q.172, B:F.179, B:Y.354, B:L.360, B:F.364 Hydrogen bonds: B:Y.117, B:T.181, B:N.351 Water bridges: B:H.176, B:F.179 Salt bridges: B:H.183, B:H.183 pi-Stacking: B:H.176 Metal complexes: B:H.357

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

NAG.5: 3 residues within 4Å: Chain A: Y.23, E.35, N.36 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.35 Hydrogen bonds: A:E.35, A:N.36 NAG.6: 5 residues within 4Å: Chain A: Q.375, N.379, S.381, I.382, E.385 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.385 Water bridges: A:N.379 NAG.17: 5 residues within 4Å: Chain B: Q.375, N.379, S.381, I.382, E.385 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.385 Water bridges: B:N.379

4 x AKR: ACRYLIC ACID(Non-covalent)

AKR.7: 4 residues within 4Å: Chain A: R.209, K.212, A.240, E.241 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.239, A:E.241 Salt bridges: A:R.209, A:K.212 AKR.8: 3 residues within 4Å: Chain A: T.181, H.183, V.260 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:H.183 Hydrogen bonds: A:N.191 AKR.18: 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:R.209 Hydrogen bonds: B:E.241 Salt bridges: B:R.209, B:K.212 AKR.19: 5 residues within 4Å: Chain B: V.235, K.236, Q.239, E.250, R.253 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.235, B:K.236, B:K.236 Hydrogen bonds: B:K.236, B:E.250 Water bridges: B:R.253 Salt bridges: B:R.253

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

EDO.9: 9 residues within 4Å: Chain A: F.178, V.197, N.344, I.346, F.350, F.498, S.499, G.502, L.503 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.344 Water bridges: A:G.502 EDO.10: 5 residues within 4Å: Chain A: H.320, Q.534, S.548, F.549, S.550 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.320, A:Q.534, A:F.549, A:S.550 EDO.11: 6 residues within 4Å: Chain A: H.195, G.505, N.506, V.507 Chain B: W.108, F.111 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.195, A:V.507 Water bridges: A:N.344, A:N.344, A:N.506 EDO.12: 5 residues within 4Å: Chain A: C.4, H.7, C.15, P.122, Q.430 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.4, A:H.7 Water bridges: A:Q.430 EDO.13: 5 residues within 4Å: Chain A: Y.354, W.356, G.495, A.496, S.499 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.354, A:Y.354 EDO.14: 5 residues within 4Å: Chain A: R.89, V.318, Y.324, V.492, A.496 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.89, A:Y.324 EDO.15: 6 residues within 4Å: Chain A: K.220, Y.223, M.230, N.279, R.280, D.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.220, A:Y.223, A:Y.223 EDO.20: 8 residues within 4Å: Chain B: E.277, R.280, E.308, A.531, S.535, L.536, N.539, N.540 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.280, B:S.535, B:N.539, B:N.540 EDO.21: 8 residues within 4Å: Chain B: F.178, V.197, I.346, F.350, F.498, S.499, G.502, L.503 No protein-ligand interaction detected (PLIP) EDO.22: 6 residues within 4Å: Chain A: W.108, F.111 Chain B: H.195, G.505, N.506, V.507 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.195, B:V.507 Water bridges: B:V.197, B:N.344 EDO.23: 1 residues within 4Å: Chain B: A.80 No protein-ligand interaction detected (PLIP) EDO.24: 6 residues within 4Å: Chain B: V.85, R.89, V.318, Y.324, A.496, L.500 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.89 EDO.25: 6 residues within 4Å: Chain B: L.321, L.353, W.356, G.495, A.496, S.499 No protein-ligand interaction detected (PLIP) EDO.26: 4 residues within 4Å: Chain B: H.91, I.93, D.94, S.95 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.95 Water bridges: B:S.95 EDO.27: 8 residues within 4Å: Chain B: H.58, Q.161, L.321, R.482, A.485, I.486, F.487, V.492 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.321, B:R.482, B:R.482, B:I.486, B:F.487

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

BOG.28: 6 residues within 4Å: Chain B: E.148, K.149, L.152, R.154, R.407, E.459 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:E.148, B:K.149, B:L.152, B:R.154 Hydrogen bonds: B:R.154, B:R.407, 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