7YXD: WT AncGR2-LBD
Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment. Determined by X-ray diffraction at 2.3 Å resolution. Released 7 Dec 2022.
- Method
- X-ray diffraction
- Resolution
- 2.3 Å
- Organisms
- unidentified, Homo sapiens
- Chains
- 8
- Atoms
- 8,280
- Mol. weight
- 121.36 kDa
- Ligands
- DEX
- Released
- 7 Dec 2022
Explore 7YXD in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7YXD contains 48 α-helices and 16 β-strands across 8 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: 11 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 532-539 | 8 | |
| α-helix | 541-544 | 4 | |
| α-helix | 553-554 | 2 | |
| α-helix | 556-579 | 24 | |
| α-helix | 584-586 | 3 | |
| α-helix | 589-616 | 28 | |
| β-strand | 621-624 | 4 | 1 |
| β-strand | 627-629 | 3 | 1 |
| α-helix | 639-656 | 18 | |
| α-helix | 660-671 | 12 | |
| β-strand | 674-676 | 3 | 2 |
| α-helix | 683-702 | 20 | |
| α-helix | 713-741 | 29 | |
| α-helix | 751-765 | 15 | |
| β-strand | 769-771 | 3 | 2 |
Chains C and J: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-25 | 7 | |
Chain D: 11 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 532-539 | 8 | |
| α-helix | 541-544 | 4 | |
| α-helix | 553-554 | 2 | |
| α-helix | 556-579 | 24 | |
| α-helix | 584-586 | 3 | |
| α-helix | 589-616 | 28 | |
| β-strand | 622-624 | 3 | 3 |
| β-strand | 627-628 | 2 | 3 |
| α-helix | 639-656 | 18 | |
| α-helix | 660-671 | 12 | |
| β-strand | 674-676 | 3 | 4 |
| α-helix | 683-702 | 20 | |
| α-helix | 713-741 | 29 | |
| α-helix | 751-765 | 15 | |
| β-strand | 769-771 | 3 | 4 |
Chains F and N: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-26 | 8 | |
Chain H: 11 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 532-539 | 8 | |
| α-helix | 541-544 | 4 | |
| α-helix | 553-554 | 2 | |
| α-helix | 556-579 | 24 | |
| α-helix | 584-586 | 3 | |
| α-helix | 589-616 | 28 | |
| β-strand | 621-624 | 4 | 5 |
| β-strand | 627-629 | 3 | 5 |
| α-helix | 639-656 | 18 | |
| α-helix | 660-671 | 12 | |
| β-strand | 674-676 | 3 | 6 |
| α-helix | 683-702 | 20 | |
| α-helix | 713-741 | 29 | |
| α-helix | 751-766 | 16 | |
| β-strand | 769-771 | 3 | 6 |
Chain L: 11 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 532-539 | 8 | |
| α-helix | 541-542 | 2 | |
| α-helix | 553-554 | 2 | |
| α-helix | 556-579 | 24 | |
| α-helix | 584-586 | 3 | |
| α-helix | 589-614 | 26 | |
| β-strand | 622-624 | 3 | 7 |
| β-strand | 627-628 | 2 | 7 |
| α-helix | 639-656 | 18 | |
| α-helix | 660-671 | 12 | |
| β-strand | 674-676 | 3 | 8 |
| α-helix | 683-702 | 20 | |
| α-helix | 713-741 | 29 | |
| α-helix | 751-765 | 15 | |
| β-strand | 769-771 | 3 | 8 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Ancestral Glucocorticoid Receptor2 | A, D, H, L | protein | 248 | unidentified | A0A1X8XLE9 (AlphaFold model) |
| SHP NR Box 1 Peptide | C, F, J, N | protein | 12 | Homo sapiens | Q15466 (AlphaFold model) |
Sequence of entity 1 (A, D, H, L), FASTA
>7YXD_1 Ancestral Glucocorticoid Receptor2 (chains A, D, H, L)
FPTLISLLEVIEPEVLYSGYDSTLPDTSTRLMSTLNRLGGRQVVSAVKWAKALPGFRNLH
LDDQMTLLQYSWMSLMAFSLGWRSYKQSNGNMLCFAPDLVINEERMQLPYMYDQCQQMLK
ISSEFVRLQVSYDEYLCMKVLLLLSTVPKDGLKSQAVFDEIRMTYIKELGKAIVKREGNS
SQNWQRFYQLTKLLDSMHEMVGGLLQFCFYTFVNKSLSVEFPEMLAEIISNQLPKFKAGS
VKPLLFHQ
Sequence of entity 2 (C, F, J, N), FASTA
>7YXD_2 SHP NR Box 1 Peptide (chains C, F, J, N)
RPAILYALLSSS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| DEX | Dexamethasone | C22 H29 F O5 | 4 |
Water and common crystallization additives (NA) are not listed.
Primary citation
The multivalency of the glucocorticoid receptor ligand-binding domain explains its manifold physiological activities. Jimenez-Panizo, A., Alegre-Marti, A., Tettey, T.T. et al. Nucleic Acids Res (2022) 50:13063-13082. DOI 10.1093/nar/gkac1119 · PubMed
Other PDB entries of the same protein (UniProt A0A1X8XLE9 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6W9L 1.45 Å, Structure of the Ancestral Glucocorticoid Receptor 2 ligand binding domain in complex…
- 6W9M 1.59 Å, Structure of the Ancestral Glucocorticoid Receptor 2 ligand binding domain in complex…
- 6W9K 1.6 Å, Structure of the Ancestral Glucocorticoid Receptor 2 ligand binding domain in complex…
- 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
- 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…
- 7YXO 2.99 Å, Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment
- 7YXP 3.36 Å, Crystal structure of WT AncGR2-LBD WT bound to dexamethasone and SHP coregulator fragment
Browse structure collections
About this viewer
MolViewer shows 7YXD directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.