8QEH | pdb_00008qeh

Crystal structure of the G11 protein heterotrimer bound to FR900359 inhibitor

PDB DOI: https://doi.org/10.2210/pdb8QEH/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: 1.43 Å
R-Value Free:
0.180 (Depositor), 0.180 (DCC)
R-Value Work:
0.140 (Depositor), 0.137 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of the heterotrimeric G11 protein bound to the cyclic depsipeptides FR900359 and YM-254890

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

To be published.

Macromolecule Content

Total Structure Weight: 89.03 kDa
Atom Count: 6,966
Modelled Residue Count: 732
Deposited Residue Count: 767
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(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 LOADING

Find similar proteins by:

(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 LOADING

Find similar proteins by:

(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 LOADING

Small Molecules

Ligands 13 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP (Subject of Investigation/LOI) Query on GDP Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
UDL (Subject of Investigation/LOI) Query on UDL 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]	(2~{S},3~{R})-2-acetamido-4-methyl-3-oxidanyl-pentanoic acid C₈ H₁₅ N O₄ GIDOPHKISCKMBN-NKWVEPMBSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
HF2 (Subject of Investigation/LOI) Query on HF2 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]	(2R)-2-hydroxy-3-phenylpropanoic acid C₉ H₁₀ O₃ VOXXWSYKYCBWHO-MRVPVSSYSA-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 O [auth A] SDF format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A]	O [auth A], P [auth A]	(2S,3R)-2-amino-3-hydroxy-4-methylpentanoic acid C₆ H₁₃ N O₃ ZAYJDMWJYCTABM-CRCLSJGQSA-N		Interactions Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain O [auth A] Focus chain P [auth A]
OTH (Subject of Investigation/LOI) Query on OTH Download Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	N,O-dimethyl-L-threonine C₆ H₁₃ N O₃ ZLRWZUVKLXZLRT-UHNVWZDZSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
MAA (Subject of Investigation/LOI) Query on MAA 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]	N-methyl-L-alanine C₄ H₉ N O₂ GDFAOVXKHJXLEI-VKHMYHEASA-N		Interactions Focus chain T [auth B] Interactions & Density Focus chain T [auth B]
DAM (Subject of Investigation/LOI) Query on DAM 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]	N-METHYL-ALPHA-BETA-DEHYDROALANINE C₄ H₇ N O₂ FLEYLGCAQDCGHN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
ALA (Subject of Investigation/LOI) Query on ALA 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]	ALANINE C₃ H₇ N O₂ QNAYBMKLOCPYGJ-REOHCLBHSA-N		Interactions Focus chain U [auth B] Interactions & Density Focus chain U [auth B]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain W [auth G] SDF format, chain X [auth G] SDF format, chain Y [auth G] MOL2 format, chain W [auth G] MOL2 format, chain X [auth G] MOL2 format, chain Y [auth G] mmCIF format, chain W [auth G] mmCIF format, chain X [auth G] mmCIF format, chain Y [auth G]	W [auth G], X [auth G], Y [auth G]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain W [auth G] Focus chain X [auth G] Focus chain Y [auth G] Interactions & Density Focus chain W [auth G] Focus chain X [auth G] Focus chain Y [auth G]
PPI (Subject of Investigation/LOI) Query on PPI Download Ideal Coordinates CCD File SDF format, chain V [auth B] MOL2 format, chain V [auth B] mmCIF format, chain V [auth B]	V [auth B]	PROPANOIC ACID C₃ H₆ O₂ XBDQKXXYIPTUBI-UHFFFAOYSA-N		Interactions Focus chain V [auth B] Interactions & Density Focus chain V [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] Q [auth B] D [auth A], E [auth A], F [auth A], G [auth A], Q [auth B], R [auth B], S [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]