SMTL ID : 3qmo.1

X-ray crystal structure of NS-398 bound to the cyclooxygenase channel of cyclooxygenase-2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

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

NAG-NDG.1: 3 residues within 4Å: Chain A: Y.46, E.58, N.59 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.58 Hydrogen bonds: A:S.29, A:S.29, A:E.58, A:N.59 NAG-NDG.3: 3 residues within 4Å: Chain B: Y.46, E.58, N.59 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.46, B:E.58

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.2: 8 residues within 4Å: Chain A: E.132, N.136, Y.139, R.208, F.212 Chain B: L.230, D.231 Ligands: MAN.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.208

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

NAG-NAG-BMA.4: 8 residues within 4Å: Chain A: L.230, D.231 Chain B: E.132, N.136, S.138, Y.139, R.208, F.212 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:R.208

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: H.25, C.27, C.28, N.30, P.146, V.147, A.148, C.151, Q.453 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.127, A:A.148 GOL.6: 3 residues within 4Å: Chain A: Q.195, H.199 Ligands: HEM.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.195 GOL.7: 5 residues within 4Å: Chain A: F.134, S.135, L.137 Chain B: L.216, G.217 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.135 GOL.13: 4 residues within 4Å: Chain A: L.137, L.216 Chain B: S.135, L.137 No protein-ligand interaction detected (PLIP) GOL.14: 8 residues within 4Å: Chain B: H.25, C.27, C.28, N.30, P.146, V.147, A.148, C.151 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.28, B:A.148 GOL.15: 4 residues within 4Å: Chain B: H.199, V.283, L.286 Ligands: HEM.17 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.199

2 x NS4: N-[2-(cyclohexyloxy)-4-nitrophenyl]methanesulfonamide(Non-covalent)

NS4.8: 16 residues within 4Å: Chain A: H.81, V.108, R.112, V.341, L.344, S.345, Y.347, Y.377, W.379, F.510, M.514, V.515, G.518, A.519, S.522, L.523 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.379, A:V.515 Hydrogen bonds: A:H.81, A:R.112, A:Y.347 Water bridges: A:A.519, A:S.522 NS4.16: 16 residues within 4Å: Chain B: H.81, V.108, R.112, V.341, L.344, S.345, Y.347, L.351, Y.377, W.379, F.510, M.514, V.515, G.518, A.519, L.523 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.344, B:Y.377, B:W.379, B:W.379, B:V.515 Hydrogen bonds: B:H.81, B:R.112 Water bridges: B:A.519, B:S.522

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

HEM.9: 20 residues within 4Å: Chain A: Y.140, A.191, A.194, Q.195, T.198, H.199, F.202, K.203, T.204, V.287, N.374, Y.377, H.378, W.379, H.380, L.383, F.396, L.400, V.439 Ligands: GOL.6 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:A.194, A:Q.195, A:F.202, A:V.287, A:Y.377, A:W.379, A:L.383, A:F.396, A:L.400, A:V.439, A:V.439 Hydrogen bonds: A:T.204, A:T.204, A:N.374, A:Q.446 Salt bridges: A:H.206, A:H.378 pi-Stacking: A:H.199, A:H.378 Metal complexes: A:H.380 HEM.17: 18 residues within 4Å: Chain B: A.191, F.192, Q.195, H.199, F.202, K.203, T.204, H.206, V.287, N.374, Y.377, H.378, W.379, H.380, L.383, V.439, Q.446 Ligands: GOL.15 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:F.192, B:Q.195, B:F.202, B:V.287, B:Y.377, B:W.379, B:L.383, B:V.439 Hydrogen bonds: B:Y.140, B:T.204, B:N.374, B:Q.446 Salt bridges: B:H.206 pi-Stacking: B:H.199, B:H.378 Metal complexes: B:H.380

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

NAG.10: 4 residues within 4Å: Chain A: Q.398, N.402, S.404, I.405 No protein-ligand interaction detected (PLIP) NAG.18: 3 residues within 4Å: Chain B: Q.398, N.402, I.405 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.402

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

BOG.11: 8 residues within 4Å: Chain A: E.171, K.172, L.175, R.176, R.177, R.430, E.478, E.482 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:E.171, A:L.175 Hydrogen bonds: A:K.172, A:R.177, A:R.430, A:E.478, A:E.482, A:E.482 Salt bridges: A:R.177, A:R.430

1 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.12: 2 residues within 4Å: Chain B: H.234 Ligands: NAG-NAG.2 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vecchio, A.J. et al., The structure of NS-398 bound to cyclooxygenase-2. J.Struct.Biol. (2011)

Release Date

2011-08-03

Peptides

Prostaglandin G/H synthase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Prostaglandin G/H synthase 2

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