SMTL ID : 8qeg.1

Crystal structure of the G11 protein heterotrimer bound to YM-254890 inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 19 residues within 4Å: Chain A: T.40, G.41, E.42, S.43, G.44, K.45, S.46, T.47, S.149, L.173, R.174, R.176, N.267, K.268, D.270, L.271, C.323, A.324, T.325 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:E.42, A:S.43, A:G.44, A:K.45, A:S.46, A:S.46, A:T.47, A:T.47, A:S.149, A:L.173, A:R.174, A:R.174, A:N.267, A:K.268, A:K.268, A:A.324 Water bridges: A:K.45, A:K.45, A:K.45, A:S.46, A:S.147, A:D.148, A:R.174 Salt bridges: A:K.45, A:R.176, A:R.176, A:D.270 pi-Cation interactions: A:K.268

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: K.269, F.321, N.329, F.332, V.333 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.269, A:F.321, A:N.329 EDO.3: 6 residues within 4Å: Chain A: S.46, R.176, V.177, I.183, G.200, G.201 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.46, A:S.46, A:R.176, A:V.177 EDO.4: 3 residues within 4Å: Chain A: E.242, Y.284, F.285 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.242 Water bridges: A:E.287 EDO.5: 2 residues within 4Å: Chain A: R.206, Y.254 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.206 EDO.6: 4 residues within 4Å: Chain A: E.287, F.301, K.304, D.308 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.308 EDO.13: 5 residues within 4Å: Chain B: G.68, T.69, D.70, L.73, G.113 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.69, B:T.69, B:T.69, B:D.70 Water bridges: B:G.113 EDO.14: 5 residues within 4Å: Chain B: R.26, F.226, T.227, Q.263, E.264 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.26, B:T.227, B:T.227, B:E.264 Water bridges: B:T.227, B:E.264 EDO.15: 7 residues within 4Å: Chain B: G.145, H.146, T.147, D.167, T.169, Q.180, T.183 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.146, B:T.147, B:Q.180, B:Q.180

1 x DAM: N-METHYL-ALPHA-BETA-DEHYDROALANINE(Non-covalent)

DAM.7: 9 residues within 4Å: Chain A: I.49, R.53, Y.60, Y.185 Ligands: HF2.8, THC.9, HL2.12, MAA.16, ALA.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.53

1 x HF2: (2R)-2-hydroxy-3-phenylpropanoic acid(Non-covalent)

HF2.8: 12 residues within 4Å: Chain A: S.46, I.49, K.50, R.53, Y.60, F.68, V.177, I.183 Ligands: DAM.7, THC.9, OTH.10, HL2.11 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.49, A:K.50, A:V.177, A:V.177, A:I.183 Hydrogen bonds: A:R.53

1 x THC: N-METHYLCARBONYLTHREONINE(Non-covalent)

THC.9: 10 residues within 4Å: Chain A: R.53, D.64, G.67, F.68 Ligands: DAM.7, HF2.8, OTH.10, HL2.11, MAA.16, ALA.17 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.68 Hydrogen bonds: A:R.53, A:R.53

1 x OTH: N,O-dimethyl-L-threonine(Non-covalent)

OTH.10: 7 residues within 4Å: Chain A: V.177, P.178, T.179 Ligands: HF2.8, THC.9, HL2.11, MAA.16 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.177

2 x HL2: (2S,3R)-2-amino-3-hydroxy-4-methylpentanoic acid(Non-covalent)

HL2.11: 7 residues within 4Å: Chain A: I.183 Ligands: HF2.8, THC.9, OTH.10, HL2.12, MAA.16, ALA.17 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.183 Water bridges: B:R.100 HL2.12: 10 residues within 4Å: Chain A: I.182, I.183, E.184 Chain B: R.100, D.122 Ligands: DAM.7, HL2.11, MAA.16, ALA.17, ACE.18 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.182, B:R.100, B:D.122 Hydrogen bonds: A:E.184

1 x MAA: N-methyl-L-alanine(Non-covalent)

MAA.16: 8 residues within 4Å: Chain A: R.53 Chain B: R.100 Ligands: DAM.7, THC.9, OTH.10, HL2.11, HL2.12, ALA.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.100, B:R.100

1 x ALA: ALANINE(Non-covalent)

ALA.17: 10 residues within 4Å: Chain A: E.184, Y.185, P.186 Chain B: R.100 Ligands: DAM.7, THC.9, HL2.11, HL2.12, MAA.16, ACE.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.100

1 x ACE: ACETYL GROUP(Non-functional Binders)

ACE.18: 5 residues within 4Å: Chain A: E.184, P.186 Chain B: R.100 Ligands: HL2.12, ALA.17 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Water bridges: B:R.100 Hydrophobic interactions: A.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muehle, J. et al., Structural analysis of G protein inhibition by cyclic depsipeptide inhibitors. To Be Published

Release Date

2025-03-19

Peptides

Guanine nucleotide-binding protein subunit alpha-11: 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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
G

Guanine nucleotide-binding protein subunit alpha-11

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

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