SMTL ID : 8j6p.1

Cryo-EM structure of the MK-6892-bound human HCAR2-Gi1 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x IX8: 7-methyl-N-[(2R)-1-phenoxypropan-2-yl]-3-(4-propan-2-ylphenyl)pyrazolo[1,5-a]pyrimidine-6-carboxamide(Non-covalent)

IX8.1: 12 residues within 4Å: Chain E: C.176, H.177, T.178, F.179, Q.180, E.183, A.184, L.187, L.188, F.191, F.248, L.251 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:H.177, E:F.179, E:E.183, E:L.187, E:F.191, E:F.248, E:F.248, E:L.251 Hydrogen bonds: E:Q.180 pi-Stacking: E:H.177, E:F.248, E:F.248

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 8 residues within 4Å: Chain E: W.52, F.60, N.61, V.64, M.102, A.138, C.142, W.145 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:F.60, E:F.60, E:V.64, E:A.138, E:W.145 CLR.4: 12 residues within 4Å: Chain E: F.58, Q.105, I.109, T.112, V.113, V.116, D.117, L.144, L.188, E.189, L.192, P.193 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:F.58, E:T.112, E:V.116, E:V.116, E:L.144, E:L.188, E:L.192 Hydrogen bonds: E:Q.105

1 x NIO: NICOTINIC ACID(Non-covalent)

NIO.3: 11 residues within 4Å: Chain E: L.76, Y.80, W.84, L.97, L.100, R.104, S.171, S.172, F.173, L.273, Y.277 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:L.97, E:L.100, E:F.173 Hydrogen bonds: E:S.172, E:S.172, E:Y.277 Salt bridges: E:R.104

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.5: 1 residues within 4Å: Chain E: N.10 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:N.10 Hydrogen bonds: E:N.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mao, C. et al., Orthosteric and allosteric modulation of human HCAR2 signaling complex. Nat Commun (2023)

Release Date

2023-12-06

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
single Fab chain (scFv16): D
Hydroxycarboxylic acid receptor 2: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
G

D
S

E
R

Membrane

We predict this structure to be a membrane protein.
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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

single Fab chain (scFv16)

Hydroxycarboxylic acid receptor 2

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