8QEG | pdb_00008qeg

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

PDB DOI: https://doi.org/10.2210/pdb8QEG/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2023-08-31 Released: 2025-03-19
Deposition Author(s): Muehle, J., Rodrigues, M.J., Guixa-Gonzalez, R., Deupi, X., Schertler, G.F.X.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.188 (Depositor), 0.196 (DCC)
R-Value Work:
0.160 (Depositor), 0.172 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structural analysis of G protein inhibition by cyclic depsipeptide inhibitors

Muehle, J., Schertler, G.F.X.

To be published.

Macromolecule Content

Total Structure Weight: 88.7 kDa
Atom Count: 6,952
Modelled Residue Count: 726
Deposited Residue Count: 767
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein subunit alpha-11	A	352	Homo sapiens	Mutation(s): 0 Gene Names: GNA11, GA11 EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P29992 (Homo sapiens) Explore P29992 Go to UniProtKB: P29992
PHAROS: P29992 GTEx: ENSG00000088256
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P29992
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	344	Homo sapiens	Mutation(s): 0 Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens) Explore P62873 Go to UniProtKB: P62873
PHAROS: P62873 GTEx: ENSG00000078369
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62873
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C [auth G]	71	Homo sapiens	Mutation(s): 1 Gene Names: GNG2
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens) Explore P59768 Go to UniProtKB: P59768
PHAROS: P59768 GTEx: ENSG00000186469
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P59768
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
HF2 (Subject of Investigation/LOI) Query on HF2 Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	(2R)-2-hydroxy-3-phenylpropanoic acid C₉ H₁₀ O₃ VOXXWSYKYCBWHO-MRVPVSSYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
THC (Subject of Investigation/LOI) Query on THC Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	N-METHYLCARBONYLTHREONINE C₆ H₁₁ N O₄ PEDXUVCGOLSNLQ-WUJLRWPWSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
HL2 (Subject of Investigation/LOI) Query on HL2 Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A]	N [auth A], O [auth A]	(2S,3R)-2-amino-3-hydroxy-4-methylpentanoic acid C₆ H₁₃ N O₃ ZAYJDMWJYCTABM-CRCLSJGQSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain N [auth A] Focus chain O [auth A]
OTH (Subject of Investigation/LOI) Query on OTH Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	N,O-dimethyl-L-threonine C₆ H₁₃ N O₃ ZLRWZUVKLXZLRT-UHNVWZDZSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
MAA (Subject of Investigation/LOI) Query on MAA Download Ideal Coordinates CCD File SDF format, chain S [auth B] MOL2 format, chain S [auth B] mmCIF format, chain S [auth B]	S [auth B]	N-methyl-L-alanine C₄ H₉ N O₂ GDFAOVXKHJXLEI-VKHMYHEASA-N		Interactions Focus chain S [auth B] Interactions & Density Focus chain S [auth B]
DAM (Subject of Investigation/LOI) Query on DAM Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	N-METHYL-ALPHA-BETA-DEHYDROALANINE C₄ H₇ N O₂ FLEYLGCAQDCGHN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
ALA (Subject of Investigation/LOI) Query on ALA Download Ideal Coordinates CCD File SDF format, chain T [auth B] MOL2 format, chain T [auth B] mmCIF format, chain T [auth B]	T [auth B]	ALANINE C₃ H₇ N O₂ QNAYBMKLOCPYGJ-REOHCLBHSA-N		Interactions Focus chain T [auth B] Interactions & Density Focus chain T [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], P [auth B], Q [auth B], R [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
ACE (Subject of Investigation/LOI) Query on ACE Download Ideal Coordinates CCD File SDF format, chain U [auth B] MOL2 format, chain U [auth B] mmCIF format, chain U [auth B]	U [auth B]	ACETYL GROUP C₂ H₄ O IKHGUXGNUITLKF-UHFFFAOYSA-N		Interactions Focus chain U [auth B] Interactions & Density Focus chain U [auth B]