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SMTL ID : 8pkm.1

Befiradol-bound serotonin 5-HT1A receptor - Gi Protein Complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.1:

10 residues within 4Å:

Chain D: Y.79, T.83, L.86, L.90, Q.141, I.428, W.431, S.435, L.438, L.439

7 PLIP interactions:

7 interactions with chain D

Hydrophobic interactions: D:L.86, D:L.90, D:I.428, D:L.438, D:L.439, D:L.439
Hydrogen bonds: D:Y.79

1 x T7M: (2R)-1-(heptadecanoyloxy)-3-{[(R)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-yl (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate(Non-covalent)

T7M.2:

12 residues within 4Å:

Chain A: D.350, C.351, G.352
Chain D: R.178, K.389, T.390, I.393, I.443, Y.444, F.447, N.448, K.449

12 PLIP interactions:

11 interactions with chain D, 1 interactions with chain A

Hydrogen bonds: D:K.386, D:T.390, D:T.390, D:I.443, D:Y.444, D:N.448, D:K.449, A:C.351
Salt bridges: D:R.178, D:K.389, D:K.389, D:K.389

1 x ZKV: (3-chloranyl-4-fluoranyl-phenyl)-[4-fluoranyl-4-[[(5-methylpyridin-2-yl)methylamino]methyl]piperidin-1-yl]methanone(Non-covalent)

ZKV.3:

17 residues within 4Å:

Chain D: V.133, A.137, W.146, F.156, I.157, D.160, V.161, C.164, C.231, I.233, S.243, A.247, W.402, F.405, F.406, N.430, Y.434

7 PLIP interactions:

7 interactions with chain D

Hydrophobic interactions: D:A.137, D:V.161, D:I.233, D:A.247, D:F.405, D:N.430
pi-Stacking: D:F.406

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Ullrich, A. et al., Discovery of a functionally selective serotonin 5-HT_1A receptor agonist for the treatment of pain. Biorxiv (2023)

Release Date

2024-05-29

Peptides

Guanine nucleotide-binding protein G(i) subunit alpha-1: A
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1: B
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2: C
5-hydroxytryptamine receptor 1A: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
G

D
R

Membrane

We predict this structure to be a membrane protein.
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Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

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

5-hydroxytryptamine receptor 1A

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Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog

Background

Transparent

Resolution

Low
Medium
High
Extreme

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