9HDF: Glucocorticoid Receptor Ligand Binding Domain

Glucocorticoid Receptor Ligand Binding Domain in complex with dexamethasone. Determined by X-ray diffraction at 2.78 Å resolution. Released 12 Nov 2025.

Method

X-ray diffraction

Resolution

2.78 Å

Organism

Homo sapiens

Chains

32

Atoms

34,585

Mol. weight

497.63 kDa

Ligands

DEX, CAC

Released

12 Nov 2025

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

Secondary structure: helices and β-sheets

9HDF contains 223 α-helices and 64 β-strands across 32 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.

Chains a, b, c, d, e, f, g, h, i, j, k, l, m, n, o and p: 1 helix, 0 β-strands

3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

>9HDF_1 Ancestral Glucocorticoid Receptor2 ligand binding domain (chains A, C, D, F, G, H, I, L, M, P)
FPTLISLLEVIEPEVLYSGYDSTLPDTSTRLMSTLNRLGGRQVVSAVKWAKALPGFRNLH
LDDQMTLLQYSWMSLMAFSLGWRSYKQSNGNMLCFAPDLVINEERMQLPYMYDQCQQMLK
ISSEFVRLQVSYDEYLCMKVLLLLSTVPKDGLKSQAVFDEIRMTYIKELGKAIVKREGNS
SQNWQRFYQLTKLLDSMHEMVGGLLQFCFYTFVNKSLSVEFPEMLAEIISNQLPKFKAGS
VKPLLFHQ

>9HDF_2 Ancestral Glucocorticoid Receptor2 ligand binding domain (chains B, E, J, K, N, O)
FPTLISLLEVIEPEVLYSGYDSTLPDTSTRLMSTLNRLGGRQVVSAVKWAKALPGFRNLH
LDDQMTLLQYSWMSLMAFSLGWRSYKQSNGNMLCFAPDLVINEERMQLPYMYDQCQQMLK
ISSEFVRLQVSYDEYLCMKVLLLLSTVPKDGLKSQAVFDEIRMTYIKELGKAIVKREGNS
SQNWQRFYQLTKLLDSMHEMVGGLLQFCFYTFVNKSLSVEFPEMLAEIISNQLPKFKAGS
VKPLLFHQ

>9HDF_3 Nuclear receptor subfamily 0 group B member 2 (chains a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p)
ASRPAILYALLSSSL

Ligands and cofactors

Water and common crystallization additives (EPE, GOL, SO4, CL, PG4, IMD, PEG, PGE) are not listed.

Primary citation

The multimerization pathway of the glucocorticoid receptor. Alegre-Marti, A., Jimenez-Panizo, A., Lafuente, A.L. et al. Nucleic Acids Res (2025) 53. DOI 10.1093/nar/gkaf1003 · PubMed

Related structures

Other PDB entries of the same protein (UniProt Q15466 (AlphaFold model), which also has an AlphaFold model), best resolution first:

• 6W9M 1.59 Å, Structure of the Ancestral Glucocorticoid Receptor 2 ligand binding domain in complex…
• 4ONI 1.8 Å, Structure of Human Orphan Receptor LRH1 bound to two bacterial phospholipids
• 1YUC 1.9 Å, Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to Phospholipid and a…
• 4DOR 1.9 Å, Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, in its apo State Bound to a…
• 5UFS 2.12 Å, X-Ray Crystal Structure of the Ancestral Glucocorticoid Receptor 2 ligand binding domain…
• 7YXC 2.25 Å, Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment
• 7YXD 2.3 Å, Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment
• 2Q3Y 2.4 Å, Ancestral Corticiod Receptor in Complex with DOC
• 7YXN 2.46 Å, Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment
• 7YXR 2.5 Å, Crystal structure of mutant AncGR2-LBD (Y545A) bound to dexamethasone and SHP…
• 2Z4J 2.6 Å, Crystal structure of AR LBD with SHP peptide NR Box 2
• 7YXO 2.99 Å, Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment

Browse structure collections

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