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SMTL ID : 8h8j.1

Lodoxamide-bound GPR35 in complex with G13

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x WYB: 2,2'-[(2-chloro-5-cyano-1,3-phenylene)bis(azanediyl)]bis(oxoacetic acid)(Non-covalent)

WYB.1:

10 residues within 4Å:

Chain C: L.12, L.76, L.79, F.162, R.163, L.236, R.239, L.257, Y.258, S.261

6 PLIP interactions:

6 interactions with chain C

Hydrophobic interactions: C:L.79, C:F.162, C:Y.258
Hydrogen bonds: C:S.261
Salt bridges: C:R.163, C:R.239

1 x CA: CALCIUM ION(Non-covalent)

CA.2:

2 residues within 4Å:

Chain C: R.163, R.254

No protein-ligand interaction detected (PLIP)

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.3:	10 residues within 4Å: Chain C: S.104, T.107, V.111, Q.131, V.135, L.139, L.142, S.146, G.178, P.182 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:T.107, C:V.111, C:V.135, C:L.142, C:P.182 Hydrogen bonds: C:S.146
CLR.4:	5 residues within 4Å: Chain C: W.51, I.56, N.60, A.133, W.140 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.51, C:A.133, C:W.140
CLR.5:	3 residues within 4Å: Chain C: V.227, A.256, I.259 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.227, C:A.256, C:I.259, C:I.259

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Duan, J. et al., Insights into divalent cation regulation and G 13 -coupling of orphan receptor GPR35. Cell Discov (2022)

Release Date

2023-02-08

Peptides

Guanine nucleotide-binding protein subunit alpha-13: A
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1: B
G-protein coupled receptor 35: 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
A

B
B

C
C

D
G

E
H

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 subunit alpha-13

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

G-protein coupled receptor 35

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

scFv16

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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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