SMTL ID : 8qeh.1

Crystal structure of the G11 protein heterotrimer bound to FR900359 inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: S.46, R.176, V.177, I.183, 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.2: 2 residues within 4Å: Chain A: R.206, W.209 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.206 Water bridges: A:Q.202 EDO.3: 2 residues within 4Å: Chain A: E.27, R.31 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.31 Water bridges: A:E.27, A:E.27 EDO.4: 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.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 EDO.16: 4 residues within 4Å: Chain B: H.229, R.255, E.264, T.267 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.255, B:R.255 Water bridges: B:H.229

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

GDP.5: 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 25 PLIP interactions: 25 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.147, A:S.149, A:L.173, A:R.174, A:R.174, A:N.267, A:K.268, A:K.268, A:A.324, A:T.325 Water bridges: A:S.46, A:D.148 Salt bridges: A:K.45, A:R.176, A:R.176, A:D.270 pi-Cation interactions: A:K.268

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 2 residues within 4Å: Chain A: H.320 Ligands: CL.7 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.320, H2O.11

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 6 residues within 4Å: Chain A: I.263, Y.318, H.320, V.337, T.340 Ligands: ZN.6 Ligand excluded by PLIP

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

DAM.8: 9 residues within 4Å: Chain A: I.49, R.53, Y.60, Y.185 Ligands: HF2.9, UDL.10, HL2.13, MAA.17, ALA.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.53

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

HF2.9: 11 residues within 4Å: Chain A: S.46, K.50, R.53, Y.60, F.68, V.177, I.183 Ligands: DAM.8, UDL.10, OTH.11, HL2.12 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.50, A:V.177, A:I.183 Hydrogen bonds: A:R.53, A:Y.60

1 x UDL: (2~{S},3~{R})-2-acetamido-4-methyl-3-oxidanyl-pentanoic acid(Non-covalent)

UDL.10: 10 residues within 4Å: Chain A: R.53, D.64, G.67, F.68 Ligands: DAM.8, HF2.9, OTH.11, HL2.12, MAA.17, ALA.18 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.11: 7 residues within 4Å: Chain A: F.68, V.177, P.178 Ligands: HF2.9, UDL.10, HL2.12, MAA.17 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)

HL2.12: 7 residues within 4Å: Chain A: I.183 Ligands: HF2.9, UDL.10, OTH.11, HL2.13, MAA.17, ALA.18 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.183 HL2.13: 9 residues within 4Å: Chain A: I.182, I.183, E.184 Chain B: R.100, D.122 Ligands: DAM.8, HL2.12, ALA.18, PPI.19 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.182, B:D.122 Hydrogen bonds: A:E.184

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

MAA.17: 7 residues within 4Å: Chain A: R.53 Chain B: R.100 Ligands: DAM.8, UDL.10, OTH.11, HL2.12, ALA.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.100, B:R.100

1 x ALA: ALANINE(Non-covalent)

ALA.18: 10 residues within 4Å: Chain A: E.184, Y.185, P.186 Chain B: R.100 Ligands: DAM.8, UDL.10, HL2.12, HL2.13, MAA.17, PPI.19 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.100

1 x PPI: PROPANOIC ACID(Non-covalent)

PPI.19: 5 residues within 4Å: Chain A: E.184, P.186 Chain B: R.100 Ligands: HL2.13, ALA.18 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:R.100 Hydrophobic interactions: A.18

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.20: 2 residues within 4Å: Chain B: R.53 Chain C: F.66 No protein-ligand interaction detected (PLIP) DMS.21: 2 residues within 4Å: Chain B: R.52 Chain C: R.62 No protein-ligand interaction detected (PLIP) DMS.22: 7 residues within 4Å: Chain B: M.329, N.344 Chain C: P.49, T.52, P.53, V.54, N.59 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muehle, J. et al., Structure of the heterotrimeric G11 protein bound to the cyclic depsipeptides FR900359 and YM-254890. 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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