SMTL ID : 6bl4.1 (1 other biounit)

Crystal Complex of Cyclooxygenase-2 with indomethacin-ethylenediamine-dansyl conjugate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.22 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: 6 residues within 4Å: Chain A: E.109, N.113, Y.116, R.185, F.189 Chain B: L.207 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:L.207 Hydrogen bonds: A:R.185 NAG-NAG.2: 7 residues within 4Å: Chain A: L.207, D.208 Chain B: E.109, N.113, Y.116, R.185, F.189 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.208, B:R.185 Hydrophobic interactions: B:F.189

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.3: 18 residues within 4Å: Chain A: 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, W.356, H.357, L.360, L.377, V.416 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:F.169, A:Q.172, A:Q.172, A:F.179, A:V.264, A:Y.354, A:W.356, A:L.360, A:L.377, A:V.416, A:V.416 Hydrogen bonds: A:Y.117, A:T.181, A:N.351 Water bridges: A:T.181, A:T.181, A:H.183 Salt bridges: A:H.183 pi-Stacking: A:H.176, A:H.355 Metal complexes: A:H.357 HEM.9: 19 residues within 4Å: Chain B: Y.117, A.168, F.169, A.171, Q.172, T.175, H.176, F.179, K.180, T.181, H.183, L.263, N.351, Y.354, H.355, W.356, H.357, L.360, V.416 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:F.169, B:A.171, B:Q.172, B:Q.172, B:F.179, B:L.263, B:W.356, B:L.360, B:L.360, B:V.416, B:V.416 Hydrogen bonds: B:Y.117, B:T.181, B:T.181, B:N.351 Water bridges: B:F.179 Salt bridges: B:H.183 pi-Stacking: B:H.176 Metal complexes: B:H.357

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

NAG.4: 5 residues within 4Å: Chain A: S.6, P.8, Y.23, E.35, N.36 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.6, A:S.6, A:Y.23, A:E.35, A:N.36 NAG.5: 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:N.379, A:E.385 NAG.10: 5 residues within 4Å: Chain B: S.6, P.8, Y.23, E.35, N.36 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.6, B:S.6, B:Y.23, B:E.35, B:N.36 Water bridges: B:T.38 NAG.11: 6 residues within 4Å: Chain B: K.374, Q.375, N.379, S.381, I.382, E.385 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.379, B:E.385, B:E.385 Water bridges: B:Y.371

2 x DXS: 2-[1-(4-chlorobenzene-1-carbonyl)-5-methoxy-2-methyl-1H-indol-3-yl]-N-[2-({[5-(dimethylamino)naphthalen-1-yl]sulfonyl}amino)ethyl]acetamide(Non-covalent)

DXS.6: 21 residues within 4Å: Chain A: V.57, H.58, L.61, Y.84, V.85, S.88, R.89, V.318, L.321, S.322, Y.324, L.353, Y.354, W.356, F.487, M.491, V.492, G.495, A.496, S.499, L.500 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:V.57, A:V.57, A:L.61, A:V.85, A:L.321, A:Y.324, A:Y.354, A:W.356, A:F.487, A:V.492, A:V.492, A:A.496, A:L.500 Hydrogen bonds: A:S.88, A:R.89, A:Y.324, A:Y.324, A:S.499 Water bridges: A:Q.161, A:E.493 pi-Stacking: A:Y.84 DXS.12: 22 residues within 4Å: Chain B: V.57, H.58, L.61, W.68, Y.84, V.85, S.88, R.89, V.318, L.321, S.322, Y.324, L.353, Y.354, W.356, F.487, M.491, V.492, G.495, A.496, S.499, L.500 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:V.57, B:V.57, B:L.61, B:Y.84, B:V.85, B:Y.324, B:Y.354, B:W.356, B:F.487, B:V.492, B:V.492, B:A.496, B:L.500 Hydrogen bonds: B:S.88, B:R.89, B:R.89, B:Y.324, B:S.499 Water bridges: B:R.482 pi-Stacking: B:Y.84 Halogen bonds: B:L.353

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

BOG.7: 3 residues within 4Å: Chain A: N.55, Y.59, F.64 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.59, A:Y.59, A:F.64 Hydrogen bonds: A:N.55 Water bridges: A:N.55 BOG.8: 8 residues within 4Å: Chain A: E.148, K.149, L.152, R.153, R.154, R.407, E.455, E.459 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:E.148, A:L.152 Hydrogen bonds: A:K.149, A:R.154, A:R.407, A:R.407, A:E.455, A:E.459, A:E.459 Water bridges: A:R.154 Salt bridges: A:K.149, A:R.154, A:R.407

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, S. et al., Fluorescent indomethacin-dansyl conjugates utilize the membrane-binding domain of cyclooxygenase-2 to block the opening to the active site. J.Biol.Chem. (2019)

Release Date

2018-11-14

Peptides

Prostaglandin G/H synthase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Prostaglandin G/H synthase 2

Related Entries With Identical Sequence