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SMTL ID : 9itb.1

LPA-bound LPAR6 in complex with miniGq

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x NKP: (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate(Non-covalent)

NKP.1:

16 residues within 4Å:

Chain D: Y.97, Y.101, T.143, V.144, S.148, F.169, E.170, N.171, F.172, W.177, I.184, F.187, I.188, V.191, Y.252, Y.273

12 PLIP interactions:

12 interactions with chain D

Hydrophobic interactions: D:Y.97, D:Y.97, D:Y.97, D:Y.101, D:I.184, D:F.187, D:F.187, D:V.191
Hydrogen bonds: D:F.169, D:N.171, D:F.172
Salt bridges: D:R.256

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.2:	6 residues within 4Å: Chain D: V.112, L.116, Y.120, K.123, L.127 Ligands: CLR.3 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:V.112, D:L.116, D:Y.120, D:L.127 Hydrogen bonds: D:K.123, D:K.123
CLR.3:	12 residues within 4Å: Chain D: Y.55, L.105, T.108, C.109, V.112, D.113, L.127, R.128, V.136, I.195 Ligands: CLR.2, PLM.5 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:L.105, D:T.108, D:V.112, D:V.112, D:V.136, D:V.136, D:I.195 Hydrogen bonds: D:D.113, D:D.113
CLR.4:	6 residues within 4Å: Chain D: I.57, N.58, L.65, K.134, W.141, I.145 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.57, D:L.65, D:I.145

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.5:

4 residues within 4Å:

Chain D: R.131, N.132, T.143
Ligands: CLR.3

3 PLIP interactions:

3 interactions with chain D

Hydrophobic interactions: D:T.143
Hydrogen bonds: D:N.132
Salt bridges: D:R.131

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

He, Y. et al., LPA-bound LPAR6 in complex with miniGq. To Be Published

Release Date

2025-01-15

Peptides

engineered miniGaq: A
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1: B
Nb35: C
Lysophosphatidic acid receptor 6: D
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
N

D
R

E
G

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

engineered miniGaq

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

Nb35

Lysophosphatidic acid receptor 6

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

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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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