SMTL ID : 3tzi.1

X-ray crystal structure of arachidonic acid bound in the cyclooxygenase channel of G533V murine COX-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

3 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: 3 residues within 4Å: Chain A: Y.29, E.41, N.42 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain B: Y.29, E.41, N.42 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain A: L.213 Chain B: E.115, N.119, Y.122, R.191, F.195 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:R.191 Water bridges: B:R.191, B:R.191, A:D.214

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: 7 residues within 4Å: Chain A: E.115, N.119, Y.122, R.191, F.195 Chain B: L.213, D.214 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.214 Water bridges: B:D.214 Hydrophobic interactions: A:R.191

2 x ACD: ARACHIDONIC ACID(Non-covalent)

ACD.5: 16 residues within 4Å: Chain A: V.91, R.95, F.180, Y.323, V.324, L.327, S.328, Y.330, Y.360, W.362, M.497, V.498, G.501, A.502, S.505, L.506 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.91, A:F.180, A:Y.323, A:V.324, A:L.327, A:Y.330, A:Y.360, A:W.362, A:W.362, A:V.498 ACD.13: 14 residues within 4Å: Chain B: V.91, F.180, Y.323, V.324, L.327, S.328, Y.330, Y.360, W.362, V.498, G.501, A.502, S.505, L.506 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.91, B:F.180, B:V.324, B:L.327, B:Y.330, B:W.362, B:A.502 Hydrogen bonds: B:A.502

2 x COH: PROTOPORPHYRIN IX CONTAINING CO(Non-covalent)

COH.6: 19 residues within 4Å: Chain A: Y.123, A.174, F.175, A.177, Q.178, H.182, F.185, K.186, T.187, H.189, V.270, N.357, Y.360, H.361, W.362, H.363, L.366, L.383, V.422 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:F.175, A:A.177, A:Q.178, A:F.185, A:F.185, A:V.270, A:Y.360, A:W.362, A:L.366, A:L.383, A:V.422, A:V.422 Hydrogen bonds: A:Y.123, A:T.187, A:N.357 Water bridges: A:T.187 Salt bridges: A:H.189 pi-Stacking: A:H.182 Metal complexes: A:H.363 COH.14: 20 residues within 4Å: Chain B: Y.123, A.174, Q.178, T.181, H.182, F.185, K.186, T.187, N.357, Y.360, H.361, W.362, H.363, L.366, F.370, L.383, V.422, A.425, Q.429 Ligands: EDO.21 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:Q.178, B:F.185, B:Y.360, B:W.362, B:L.366, B:F.370, B:V.422 Hydrogen bonds: B:T.187, B:T.187, B:N.357, B:Q.429 Water bridges: B:F.185 Salt bridges: B:H.189 pi-Stacking: B:H.182 Metal complexes: B:H.363

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

NAG.7: 4 residues within 4Å: Chain A: Q.381, N.385, S.387, I.388 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.385 NAG.15: 6 residues within 4Å: Chain B: Y.377, Q.381, N.385, S.387, I.388, E.391 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.385

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

BOG.8: 8 residues within 4Å: Chain A: E.154, K.155, L.158, R.159, R.160, R.413, E.461, E.465 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:E.154, A:L.158 Hydrogen bonds: A:K.155, A:K.155, A:R.160, A:R.413, A:E.461, A:E.461, A:E.465 Water bridges: A:E.465 Salt bridges: A:K.155, A:R.160

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

EDO.9: 7 residues within 4Å: Chain A: P.137, M.138, L.146, S.430, R.431, K.434, Y.435 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.435, A:Y.435 Water bridges: A:E.477 EDO.10: 8 residues within 4Å: Chain A: E.283, R.286, E.314, A.537, S.541, L.542, N.545, N.546 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.283, A:R.286, A:S.541, A:N.545, A:N.546 Water bridges: A:S.541 EDO.16: 5 residues within 4Å: Chain B: K.226, Y.229, V.236, N.285, D.289 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.226, B:K.226, B:N.285 EDO.17: 7 residues within 4Å: Chain B: P.137, M.138, L.146, S.430, R.431, K.434, Y.435 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.477 EDO.18: 4 residues within 4Å: Chain B: R.215, K.218, V.246, E.247 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.215, B:K.218, B:E.247 EDO.19: 4 residues within 4Å: Chain A: S.118, L.120 Chain B: L.120, L.199 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.118 EDO.20: 5 residues within 4Å: Chain B: K.150, L.153, Q.420, A.421, K.424 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.150, B:K.150 EDO.21: 4 residues within 4Å: Chain B: Q.178, L.269, V.270 Ligands: COH.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.178, B:L.269

2 x AKR: ACRYLIC ACID(Non-covalent)

AKR.11: 4 residues within 4Å: Chain A: S.452, F.453, E.454, K.467 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.453, A:K.467 Hydrogen bonds: A:F.453, A:E.454 AKR.12: 6 residues within 4Å: Chain A: D.214, R.215, K.218, Q.245, V.246, E.247 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.247 Water bridges: A:R.215 Salt bridges: A:R.215, A:K.218

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vecchio, A.J. et al., Investigating Substrate Promiscuity in Cyclooxygenase-2: THE ROLE OF ARG-120 AND RESIDUES LINING THE HYDROPHOBIC GROOVE. J.Biol.Chem. (2012)

Release Date

2012-04-25

Peptides

Prostaglandin G/H synthase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Prostaglandin G/H synthase 2