SMTL ID : 6bl3.2 (1 other biounit)

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

Coordinates

PDB Format

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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.185 NAG-NAG.2: 6 residues within 4Å: Chain A: L.207 Chain B: E.109, N.113, Y.116, R.185, F.189 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.185

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

NAG.3: 5 residues within 4Å: Chain A: S.6, P.8, Y.23, E.35, N.36 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.8 Water bridges: A:P.8, A:N.36 NAG.4: 6 residues within 4Å: Chain A: K.374, Q.375, N.379, S.381, I.382, E.385 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.379 NAG.9: 5 residues within 4Å: Chain B: S.6, P.8, Y.23, E.35, N.36 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.8 Hydrogen bonds: B:Y.23, B:N.36 Water bridges: B:N.36 NAG.10: 5 residues within 4Å: Chain B: K.374, Q.375, N.379, S.381, I.382 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.379

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

HEM.5: 20 residues within 4Å: Chain A: Y.117, A.168, A.171, 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.359, L.360, F.364, L.377, V.416 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:A.171, A:Q.172, A:Q.172, A:F.179, A:V.264, A:W.356, A:L.359, A:L.360, A:F.364, A:L.377, A:V.416, A:V.416 Hydrogen bonds: A:T.181, A:T.181, A:N.351, A:N.351 Salt bridges: A:H.183 pi-Stacking: A:H.176 Metal complexes: A:H.357 HEM.11: 20 residues within 4Å: Chain B: Y.117, A.168, A.171, 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.359, L.360, F.364, L.377, V.416 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:A.171, B:Q.172, B:F.179, B:V.264, B:W.356, B:L.359, B:L.360, B:F.364, B:L.377, B:V.416, B:V.416 Hydrogen bonds: B:Y.117, B:T.181, B:N.351, B:N.351 Salt bridges: B:H.183 pi-Stacking: B:H.176 Metal complexes: B:H.357

2 x L7M: 2-[1-(4-chlorobenzene-1-carbonyl)-5-methoxy-2-methyl-1H-indol-3-yl]-N-[4-({[5-(dimethylamino)naphthalen-1-yl]sulfonyl}amino)butyl]acetamide(Non-covalent)

L7M.6: 22 residues within 4Å: Chain A: V.57, H.58, I.81, 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, E.493, G.495, A.496, S.499, L.500 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:V.57, A:V.57, A:I.81, A:Y.84, 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:L.500 Hydrogen bonds: A:S.88, A:R.89, A:Y.324, A:Y.324, A:S.499 Halogen bonds: A:L.353 L7M.12: 25 residues within 4Å: Chain B: P.52, V.57, H.58, I.60, L.61, I.81, 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, E.493, G.495, A.496, S.499, L.500 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:P.52, B:V.57, B:V.57, B:L.61, B:L.61, B:I.81, 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:L.500 Hydrogen bonds: B:S.88, B:R.89, B:Y.324, B:S.499 Water bridges: B:Q.161, B:R.482 Halogen bonds: B:L.353

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

BOG.7: 5 residues within 4Å: Chain A: N.55, T.56, Y.59, K.480, P.483 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.56 Hydrogen bonds: A:N.55, A:K.480, A:K.480 BOG.8: 7 residues within 4Å: Chain A: E.148, K.149, R.153, R.154, R.407, E.455, E.459 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.148, A:R.154 Hydrogen bonds: A:R.154, A:R.407, A:E.455, A:E.459 Salt bridges: A:R.154, A:R.407 BOG.13: 5 residues within 4Å: Chain B: N.55, T.56, Y.59, K.480, P.483 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:T.56, B:Y.59 Hydrogen bonds: B:K.480, B:K.480

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
C

B
D

Prostaglandin G/H synthase 2

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