SMTL ID : 8f7r.1

Gi bound mu-opioid receptor in complex with endomorphin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-1-1-1-mer

Ligands

2 x TYR- PRO- TRP- PHE- NH2: endomorphin(Non-covalent)

TYR-PRO-TRP-PHE-NH2.1: 17 residues within 4Å: Chain A: Q.133, N.136, Y.137, W.142, V.152, I.153, D.156, Y.157, M.160, C.226, K.242, V.245, V.309, W.327, H.328, I.331, Y.335 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Q.133, A:Y.137, A:W.142, A:W.142, A:V.152, A:I.153, A:Y.157, A:W.327 Hydrogen bonds: A:N.136, A:D.156, A:Y.157, A:Y.157 pi-Stacking: A:H.328 TYR-PRO-TRP-PHE-NH2.2: 19 residues within 4Å: Chain F: Y.84, Q.133, N.136, Y.137, W.142, V.152, D.156, Y.157, M.160, C.226, K.242, V.245, I.305, H.306, V.309, W.327, H.328, I.331, Y.335 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:Y.84, F:Q.133, F:Q.133, F:Y.137, F:W.142, F:V.152, F:Y.157, F:V.245, F:V.309, F:W.327, F:I.331 Hydrogen bonds: F:N.136, F:D.156, F:K.242 pi-Stacking: F:H.328

10 x CLR: CHOLESTEROL(Non-covalent)

CLR.3: 8 residues within 4Å: Chain A: M.108, N.118, L.121, L.125, Y.158, K.194, V.198, W.201 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.121, A:L.125, A:K.194, A:K.194, A:V.198, A:W.201, A:W.201 CLR.4: 4 residues within 4Å: Chain A: P.304, Y.308, I.311, S.326 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.304, A:P.304, A:Y.308, A:I.311 CLR.5: 9 residues within 4Å: Chain A: F.165, L.203, A.206, I.207, P.210, W.237, F.248 Chain F: L.203 Ligands: CLR.11 8 PLIP interactions: 1 interactions with chain F, 7 interactions with chain A Hydrophobic interactions: F:L.203, A:F.165, A:L.203, A:P.210, A:P.210, A:W.237, A:F.248, A:F.248 CLR.6: 14 residues within 4Å: Chain A: W.235, Y.236, N.239, L.240, I.243, A.313, L.314 Chain F: V.172, Y.175, I.176, H.180, K.183, I.256 Ligands: CLR.8 9 PLIP interactions: 6 interactions with chain F, 3 interactions with chain A Hydrophobic interactions: F:V.172, F:V.172, F:Y.175, F:I.176, F:K.183, F:I.256, A:Y.236, A:N.239, A:L.240 CLR.7: 12 residues within 4Å: Chain A: Y.175, M.252, L.255, I.256, V.259, L.263 Chain F: I.243, I.247, I.251, L.314 Ligands: CLR.8, CLR.12 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain F Hydrophobic interactions: A:L.255, A:I.256, A:V.259, A:V.259, A:L.263, F:I.243, F:I.243, F:I.247, F:I.247, F:I.251, F:L.314 CLR.8: 12 residues within 4Å: Chain A: I.243, I.247, I.251, L.314 Chain F: Y.175, M.252, L.255, I.256, V.259, L.263 Ligands: CLR.6, CLR.7 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain F Hydrophobic interactions: A:I.243, A:I.243, A:I.247, A:I.247, A:I.251, F:L.255, F:L.255, F:I.256, F:V.259, F:L.263 Hydrogen bonds: F:Y.175 CLR.9: 8 residues within 4Å: Chain F: M.108, N.118, L.121, L.125, Y.158, K.194, V.198, W.201 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:L.121, F:L.125, F:K.194, F:V.198, F:W.201, F:W.201, F:W.201 CLR.10: 3 residues within 4Å: Chain F: Y.308, I.311, S.326 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:Y.308, F:Y.308, F:I.311 CLR.11: 13 residues within 4Å: Chain A: L.203, F.248 Chain F: F.165, L.203, A.206, I.207, M.214, W.237, L.240, L.241, F.248, M.252 Ligands: CLR.5 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: F:F.165, F:A.206, F:W.237, F:L.240, F:L.241, F:F.248, A:L.203 CLR.12: 14 residues within 4Å: Chain A: V.172, Y.175, I.176, H.180, K.183, I.256 Chain F: W.235, Y.236, N.239, L.240, I.243, A.313, L.314 Ligands: CLR.7 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain F Hydrophobic interactions: A:V.172, A:V.172, A:Y.175, A:I.176, A:I.176, A:K.183, A:I.256, F:W.235, F:W.235, F:Y.236, F:N.239, F:L.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., Structures of the entire human opioid receptor family. Cell (2023)

Release Date

2022-12-14

Peptides

Mu-type opioid receptor: AF
Guanine nucleotide-binding protein G(i) subunit alpha-1: BG
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1: C
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2: D
scFv16: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

F
M

B
A

G
F

C
B

D
C

E
E

Membrane

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

Guanine nucleotide-binding protein G(i) subunit alpha-1

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

scFv16

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