MolNFT v1 · #66292 · protein
Crystal structure of human estrogen receptor alpha ligand-binding domain in complex with a glucocorticoid receptor interacting protein 1 nr box II peptide and estrone ((8R,9S,13S,14S)-3-hydroxy-13-methyl- 7,8,9,11,12,14,15,16-octahydro-6H-CYCLOPENTA[A]PHENANTHREN-17-one)
3HM1: “Crystal structure of human estrogen receptor alpha ligand-binding domain in complex with a glucocorticoid…”. X-ray diffraction, 1 ligand (J3Z), 9 pockets (best druggability 0.84). MolNFT v1 #66292 on GenesisL1: 3D structure, binding…
- PDB
- 3HM1
- Type
- protein
- Length
- 493 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; Nuclear receptor coactivator 2
- UniProt
- P03372, Q9WUI9
- Ligands
- J3Z
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 68% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 235 | 70% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 239 | 66% helix, 4% strand | P03372 |
| C | Nuclear receptor coactivator 2 | protein | 10 | 70% helix, 0% strand | Q9WUI9 |
| D | Nuclear receptor coactivator 2 | protein | 9 | 56% helix, 0% strand | Q9WUI9 |
Ligands and binding sites
- J3Z · (9beta,13alpha)-3-hydroxyestra-1,3,5(10)-trien-17-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.84 | 0.98 | 23 | J3Z |
| 2 | 186 | 0.83 | 0.97 | 24 | J3Z |
| 3 | 105 | 0.64 | 0.89 | 21 | empty |
| 4 | 240 | 0.60 | 0.80 | 33 | empty |
| 5 | 94 | 0.57 | 0.86 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1844 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 492 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 455 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (artifact).
Compared structures
- 3HM1 · Crystal structure of human Estrogen Receptor Alpha Ligand-Binding Domain in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- P03372 · AlphaFold monomer V2.0 prediction for estrogen receptor (P03372) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9WUI9 · AlphaFold monomer V2.0 prediction for nuclear receptor coactivator 2 (Q9WUI9) · a predicted model of the same protein · chain D against A, TM-score 0.84
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 P03372
- Every structure of UniProt Q9WUI9
- Elsewhere: RCSB PDB 3HM1 · PDBe 3HM1 · UniProt P03372 · UniProt Q9WUI9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.