MolNFT v1 · #29837 · protein
Human estrogen receptor alpha ligand-binding domain in complex with obcp-3M and a glucocorticoid receptor interacting protein 1 nr box II peptide
1ZKY: “Human estrogen receptor alpha ligand-binding domain in complex with obcp-3M and a glucocorticoid receptor…”. X-ray diffraction, 1 ligand (689), 7 pockets (best druggability 0.84). MolNFT v1 #29837 on GenesisL1: 3D structure, binding…
- PDB
- 1ZKY
- Type
- protein
- Length
- 503 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; Nuclear receptor coactivator 2
- UniProt
- P03372, Q15596
- Ligands
- 689
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 239 | 69% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 245 | 67% helix, 4% strand | P03372 |
| C | Nuclear receptor coactivator 2 | protein | 10 | 70% helix, 0% strand | Q15596 |
| D | Nuclear receptor coactivator 2 | protein | 9 | 78% helix, 0% strand | Q15596 |
Ligands and binding sites
- 689 · 4-[(1S,2S,5S)-5-(hydroxymethyl)-6,8,9-trimethyl-3-oxabicyclo[3.3.1]non-7-en-2-yl]phenol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 193 | 0.84 | 0.97 | 22 | 689 |
| 2 | 203 | 0.84 | 0.97 | 23 | 689 |
| 3 | 101 | 0.62 | 0.88 | 24 | empty |
| 4 | 94 | 0.58 | 0.86 | 17 | empty |
| 5 | 295 | 0.58 | 0.77 | 34 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1978 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 532 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 496 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (artifact).
Compared structures
- 1ZKY · Human Estrogen Receptor Alpha Ligand-Binding Domain In Complex With OBCP-3M and A… · the same entry in another collection · chain A against A, 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
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 Q15596
- Elsewhere: RCSB PDB 1ZKY · PDBe 1ZKY · UniProt P03372 · UniProt Q15596
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