SMTL ID : 4dkl.1

Crystal structure of the mu-opioid receptor bound to a morphinan antagonist

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x BF0: methyl 4-{[(5beta,6alpha)-17-(cyclopropylmethyl)-3,14-dihydroxy-4,5-epoxymorphinan-6-yl]amino}-4-oxobutanoate(Covalent)

BF0.1: 14 residues within 4Å: Chain A: D.96, Y.97, M.100, E.178, K.182, V.185, W.396, I.399, H.400, V.403, K.406, W.421, I.425, Y.429 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.97, A:K.182, A:W.396, A:V.403, A:I.425, A:Y.429 Hydrogen bonds: A:D.96, A:D.96 Water bridges: A:Y.429 Salt bridges: A:D.96, A:K.182, A:K.406 BF0.19: 14 residues within 4Å: Chain B: D.96, Y.97, M.100, E.178, K.182, V.185, W.396, I.399, H.400, V.403, K.406, W.421, I.425, Y.429 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.97, B:K.182, B:W.396, B:V.403, B:I.425, B:Y.429 Hydrogen bonds: B:D.96 Salt bridges: B:D.96, B:K.182, B:K.406

24 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: T.50, A.51, T.52, R.114, R.128, I.381 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: N.86, K.90, A.155, T.156 Ligand excluded by PLIP SO4.4: 7 residues within 4Å: Chain A: H.120, P.121, V.122, K.123, R.219, G.223, L.224 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: R.225, L.226, K.227 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: H.172, P.173, T.174, W.175 Ligand excluded by PLIP SO4.7: 6 residues within 4Å: Chain A: G.324, F.325, T.326, N.327, S.328, N.343 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Chain A: S.347, R.348 Ligand excluded by PLIP SO4.9: 2 residues within 4Å: Chain A: R.330, Q.334 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain A: R.380, R.383 Ligand excluded by PLIP SO4.11: 5 residues within 4Å: Chain A: H.120, R.207, R.219, L.224, K.271 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain A: T.353, P.354, N.355, R.356 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain A: R.44, Y.45, T.46 Ligand excluded by PLIP SO4.20: 6 residues within 4Å: Chain B: T.50, A.51, T.52, R.114, R.128, I.381 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain B: N.86, K.90, A.155, T.156 Ligand excluded by PLIP SO4.22: 7 residues within 4Å: Chain B: H.120, P.121, V.122, K.123, R.219, G.223, L.224 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain B: R.225, L.226, K.227 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain B: H.172, P.173, T.174, W.175 Ligand excluded by PLIP SO4.25: 6 residues within 4Å: Chain B: G.324, F.325, T.326, N.327, S.328, N.343 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain B: S.347, R.348 Ligand excluded by PLIP SO4.27: 2 residues within 4Å: Chain B: R.330, Q.334 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain B: R.380, R.383 Ligand excluded by PLIP SO4.29: 5 residues within 4Å: Chain B: H.120, R.207, R.219, L.224, K.271 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain B: T.353, P.354, N.355, R.356 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain B: R.44, Y.45, T.46 Ligand excluded by PLIP

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.14: 8 residues within 4Å: Chain A: T.397, P.398, I.401, Y.402, I.405, I.411, F.416, S.420 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.397, A:P.398, A:I.401, A:Y.402, A:Y.402, A:I.405, A:I.411, A:F.416 CLR.32: 8 residues within 4Å: Chain B: T.397, P.398, I.401, Y.402, I.405, I.411, F.416, S.420 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:T.397, B:P.398, B:I.401, B:Y.402, B:Y.402, B:I.405, B:I.411, B:F.416

4 x MPG: [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate(Non-covalent)

MPG.15: 5 residues within 4Å: Chain A: F.57, N.58, K.134, N.137, W.141 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.57, A:N.137, A:W.141, A:W.141, A:W.141 Hydrogen bonds: A:K.134 Salt bridges: A:K.49, A:K.134 MPG.16: 8 residues within 4Å: Chain A: M.21, Y.24, S.25, C.28, L.32, L.70, P.71, S.74 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.32, A:P.71 Hydrogen bonds: A:M.21, A:Y.24, A:S.74 MPG.33: 5 residues within 4Å: Chain B: F.57, N.58, K.134, N.137, W.141 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.57, B:N.137, B:W.141, B:W.141, B:W.141 Hydrogen bonds: B:K.134 Salt bridges: B:K.49, B:K.134 MPG.34: 8 residues within 4Å: Chain B: M.21, Y.24, S.25, C.28, L.32, L.70, P.71, S.74 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.32, B:P.71 Hydrogen bonds: B:M.21, B:Y.24, B:S.74

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.17: 13 residues within 4Å: Chain A: W.175, K.406, A.407, L.408, I.409, T.410 Chain B: W.175, K.406, A.407, L.408, I.409, T.410 Ligands: 1PE.35 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.406 1PE.35: 13 residues within 4Å: Chain A: W.175, K.406, A.407, L.408, I.409, T.410 Chain B: W.175, K.406, A.407, L.408, I.409, T.410 Ligands: 1PE.17 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.406

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.18: 3 residues within 4Å: Chain A: S.210, E.373, K.374 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain B: S.210, E.373, K.374 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manglik, A. et al., Crystal structure of the {mu}-opioid receptor bound to a morphinan antagonist. Nature (2012)

Release Date

2012-03-21

Peptides

Mu-type opioid receptor, lysozyme chimera: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Membrane

We predict this structure to be a membrane protein.
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Mu-type opioid receptor, lysozyme chimera