9KND: Human ERRg LBD

Crystal structure of human ERRg LBD in complex with indole. Determined by X-ray diffraction at 1.52 Å resolution. Released 16 Apr 2025.

Method: X-ray diffraction
Resolution: 1.52 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,247
Mol. weight: 30.2 kDa
Ligands: IND
Released: 16 Apr 2025

Explore 9KND in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9KND contains 14 α-helices and 2 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	236-243	8
α-helix	245-248	4
α-helix	258-259	2
α-helix	261-283	23
α-helix	289-291	3
α-helix	294-316	23
β-strand	324-327	4	1
β-strand	330-332	3	1
α-helix	334-340	7
α-helix	343-359	17
α-helix	363-375	13
α-helix	385-406	22
α-helix	413-418	6
α-helix	421-441	21
α-helix	448-455	8

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	379-385	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Estrogen-related receptor gamma	A	protein	251	Homo sapiens	P62508 (AlphaFold model)
Nuclear receptor-interacting protein 1	B	protein	15	Homo sapiens	P48552 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9KND_1 Estrogen-related receptor gamma (chains A)
MGSSHHHHHHSSGLVPRGSHMPAKKPYNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTT
LCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVYA
DDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEA
VQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPMH
KLFLEMLEAKV

Sequence of entity 2 (B), FASTA

>9KND_2 Nuclear receptor-interacting protein 1 (chains B)
NNSLLLHLLKSQTIP

Ligands and cofactors

ID	Name	Formula	Copies
IND	Indole	C8 H7 N	1

Primary citation

Identification of indoles as potential endogenous ligands of ERR gamma and their modulation on drug binding. Shuai, Y.Y., Zhang, H.Y., Chen, R. et al. Acta Pharmacol Sin (2025) 46:2574-2582. DOI 10.1038/s41401-025-01550-6 · PubMed

Other PDB entries of the same protein (UniProt P62508 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6XXC 1.3 Å, Ternary complex of 14-3-3 sigma (C38N), Estrogen Related Receptor gamma (DBD)…
6XY5 1.3 Å, Ternary complex of 14-3-3 sigma (C38N), Estrogen Related Receptor gamma (DBD)…
6Y18 1.3 Å, Ternary complex of 14-3-3 sigma (C38N), Estrogen Related Receptor gamma (DBD)…
6Y3W 1.34 Å, Ternary complex of 14-3-3 sigma (C38N), Estrogen Related Receptor gamma (DBD)…
6Y1D 1.38 Å, Binary complex of 14-3-3 sigma (C38N) with the Estrogen Related Receptor gamma (DBD)…
8B4Q 1.4 Å, Ternary structure of 14-3-3s, ERRg phosphopeptide and dual-reactive compound 5
8BJG 1.4 Å, Ternary structure of 14-3-3s, ERRg phosphopeptide and dual-reactive compound 8
8BJN 1.4 Å, Ternary structure of 14-3-3s, ERRg phosphopeptide and dual-reactive compound 6
8BM5 1.4 Å, Ternary structure of 14-3-3s, ERRg phosphopeptide and dual-reactive compound 7
6I65 1.5 Å, Crystal structure of human ERRg LBD in complex with 4-iso-propylphenol
9KNG 1.5 Å, Crystal structure of human ERRg LBD in complex with 4034496
2E2R 1.6 Å, Crystal structure of human estrogen-related receptor gamma ligand binding domain complex…

Browse structure collections

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