MolNFT v1 · #14240 · protein
Crystal structure of a dimer complex of the human glucocorticoid receptor ligand-binding domain bound to dexamethasone and a TIF2 coactivator motif
1M2Z: “Crystal structure of a dimer complex of the human glucocorticoid receptor ligand-binding domain bound to…”. X-ray diffraction, 1 ligand (DEX), 8 pockets (best druggability 0.84). MolNFT v1 #14240 on GenesisL1: 3D structure, binding…
- PDB
- 1M2Z
- Type
- protein
- Length
- 550 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucocorticoid receptor; Nuclear receptor coactivator 2
- UniProt
- P04150, Q15596
- Ligands
- DEX
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 63% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucocorticoid receptor | protein | 255 | 64% helix, 5% strand | P04150 |
| B, E | Nuclear receptor coactivator 2 | protein | 21 | 29% helix, 0% strand | Q15596 |
| D | Glucocorticoid receptor | protein | 253 | 64% helix, 6% strand | P04150 |
Ligands and binding sites
- DEX · Dexamethasone · ligand · 2 copies · chains A, D
- BOG · octyl beta-D-glucopyranoside · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.84 | 0.97 | 30 | DEX |
| 2 | 209 | 0.84 | 0.96 | 24 | DEX |
| 3 | 348 | 0.65 | 0.80 | 36 | empty |
| 4 | 337 | 0.64 | 0.79 | 34 | empty |
| 5 | 55 | 0.50 | 0.87 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 732 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 692 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 620 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1M2Z · Crystal structure of a dimer complex of the human glucocorticoid receptor ligand-binding… · the same entry in another collection · chain A against A, TM-score 1.00
- P04150 · AlphaFold monomer V2.0 prediction for glucocorticoid receptor (P04150) · a predicted model of the same protein · chain D against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P04150
- Every structure of UniProt Q15596
- Elsewhere: RCSB PDB 1M2Z · PDBe 1M2Z · UniProt P04150 · UniProt Q15596
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