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SMTL ID : 7y12.1

Cryo-EM structure of MrgD-Gi complex with beta-alanine

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x BAL: BETA-ALANINE(Non-covalent)

BAL.1:

7 residues within 4Å:

Chain D: R.228, C.289, C.300, D.304, W.366, Y.370, W.371

4 PLIP interactions:

4 interactions with chain D

Hydrophobic interactions: D:W.366, D:Y.370
Hydrogen bonds: D:W.366
Salt bridges: D:R.228

3 x PLM: PALMITIC ACID(Non-covalent)

PLM.2:	5 residues within 4Å: Chain D: I.188, N.192, H.265, A.268, W.275 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:A.268, D:W.275, D:W.275, D:W.275 Salt bridges: D:H.265
PLM.3:	3 residues within 4Å: Chain D: F.254, I.256, W.257 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.254, D:F.254, D:I.256, D:W.257, D:W.257, D:W.257
PLM.4:	8 residues within 4Å: Chain D: Y.189, A.243, T.246, Q.247, L.250, R.262, L.266, V.314 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:A.243, D:T.246, D:L.250, D:V.314, D:V.314 Hydrogen bonds: D:Y.189 Salt bridges: D:R.262

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Suzuki, S. et al., Structural insight into the activation mechanism of MrgD with heterotrimeric Gi-protein revealed by cryo-EM. Commun Biol (2022)

Release Date

2022-07-20

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
Soluble cytochrome b562,Mas-related G-protein coupled receptor member D: D
scFV16: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
R

E
S

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

Soluble cytochrome b562,Mas-related G-protein coupled receptor member D

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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