SMTL ID : 3krk.1

X-ray crystal structure of arachidonic acid bound in the cyclooxygenase channel of L531F murine COX-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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.27, E.39, N.40 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 7 residues within 4Å: Chain A: E.113, N.117, Y.120, R.189, F.193 Chain B: L.211, D.212 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:R.189 Hydrogen bonds: A:R.189 Water bridges: B:D.212 NAG-NAG.3: 3 residues within 4Å: Chain B: Y.27, E.39, N.40 No protein-ligand interaction detected (PLIP)

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(Non-functional Binders)

NAG-NAG-MAN.4: 7 residues within 4Å: Chain A: L.211, D.212 Chain B: E.113, N.117, Y.120, R.189, F.193 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:R.189 Water bridges: A:D.212, A:D.212, A:D.212, A:D.212

2 x ACD: ARACHIDONIC ACID(Non-covalent)

ACD.5: 22 residues within 4Å: Chain A: R.93, F.178, F.182, V.201, Y.321, V.322, L.325, S.326, Y.328, N.348, I.350, F.354, Y.358, W.360, M.495, V.496, G.499, A.500, S.503, F.504, G.506, L.507 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.178, A:F.178, A:F.182, A:F.182, A:V.201, A:Y.321, A:V.322, A:V.322, A:L.325, A:I.350, A:F.354, A:W.360, A:W.360, A:V.496, A:A.500, A:L.507, A:L.507 Salt bridges: A:R.93 ACD.13: 23 residues within 4Å: Chain B: R.93, F.178, F.182, V.317, Y.321, V.322, L.325, S.326, Y.328, N.348, I.350, F.354, Y.358, W.360, M.495, V.496, G.499, A.500, F.502, S.503, F.504, G.506, L.507 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.178, B:F.178, B:F.182, B:F.182, B:V.317, B:V.322, B:L.325, B:I.350, B:F.354, B:F.354, B:W.360, B:W.360, B:V.496, B:L.507 Hydrogen bonds: B:Y.328 Salt bridges: B:R.93

4 x AKR: ACRYLIC ACID(Non-covalent)

AKR.6: 4 residues within 4Å: Chain A: S.450, F.451, E.452, K.465 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.451, A:K.465 Hydrogen bonds: A:F.451, A:E.452 AKR.7: 6 residues within 4Å: Chain A: D.212, R.213, K.216, Q.243, V.244, E.245 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.213, A:R.213 Hydrogen bonds: A:E.245 Salt bridges: A:R.213, A:K.216 AKR.14: 4 residues within 4Å: Chain B: S.450, F.451, E.452, K.465 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.451, B:K.465 Hydrogen bonds: B:F.451, B:E.452, B:A.461 Water bridges: B:E.452 Salt bridges: B:K.465 AKR.15: 6 residues within 4Å: Chain B: T.210, R.213, K.216, Q.243, V.244, E.245 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:R.213 Hydrogen bonds: B:E.245 Salt bridges: B:R.213, B:K.216

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 7 residues within 4Å: Chain A: H.6, C.8, C.9, P.127, V.128, A.129, C.132 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.6, A:P.126, A:A.129, A:Q.434 GOL.12: 7 residues within 4Å: Chain A: R.16, T.32, R.33, T.34, Y.95 Chain B: Q.516, K.519 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:K.519, A:R.33, A:Y.95 Water bridges: B:Q.516, A:R.16, A:R.16, A:R.16, A:T.34 GOL.16: 8 residues within 4Å: Chain B: H.6, C.8, C.9, P.127, V.128, A.129, C.132, Q.434 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.126, B:A.129, B:Q.434

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

COH.9: 15 residues within 4Å: Chain A: A.175, Q.176, H.180, F.183, T.185, H.187, L.267, N.355, Y.358, H.359, W.360, H.361, L.364, V.420, Q.427 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:A.175, A:Q.176, A:Q.176, A:F.183, A:W.360, A:L.364 Hydrogen bonds: A:T.185, A:T.185, A:Q.427 Salt bridges: A:H.187, A:H.187 pi-Cation interactions: A:H.361 COH.17: 16 residues within 4Å: Chain B: A.172, F.173, A.175, Q.176, H.180, F.183, T.185, H.187, L.267, V.268, N.355, Y.358, H.359, H.361, L.364, L.381 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:F.173, B:A.175, B:Q.176, B:Q.176, B:L.267, B:V.268, B:V.268, B:Y.358, B:L.364, B:L.381 Hydrogen bonds: B:T.185, B:T.185, B:T.185 Water bridges: B:Q.427 Salt bridges: B:H.180, B:H.187 pi-Stacking: B:H.359, B:H.361 Metal complexes: B:H.361

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

NAG.10: 6 residues within 4Å: Chain A: K.378, Q.379, N.383, S.385, I.386, E.389 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.389, A:E.389 NAG.18: 5 residues within 4Å: Chain B: Q.379, N.383, S.385, I.386, E.389 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.383 Water bridges: B:N.383

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

BOG.11: 7 residues within 4Å: Chain A: E.152, K.153, R.157, R.158, R.411, E.459, E.463 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.152 Hydrogen bonds: A:R.158, A:R.411, A:R.411, A:E.463 Water bridges: A:E.463 Salt bridges: A:K.153, A:R.158 BOG.19: 6 residues within 4Å: Chain B: E.152, L.156, R.157, R.158, I.415, Q.418 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.415 Hydrogen bonds: B:Q.418

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vecchio, A.J. et al., Structural basis of fatty acid substrate binding to cyclooxygenase-2. J.Biol.Chem. (2010)

Release Date

2010-05-12

Peptides

Prostaglandin G/H synthase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Prostaglandin G/H synthase 2