Research workbench
Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with 4,4',4''-(thiophene-2,3,5-TRIYL)TRIPHENOL
Analyse Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TLM
- Type
- protein
- Length
- 470 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; Nuclear receptor coactivator 2
- UniProt
- P03372
- Ligands
- 7EM
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 65% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 226 | 63% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 227 | 66% helix, 4% strand | P03372 |
| C | Nuclear receptor coactivator 2 | protein | 9 | 67% helix, 0% strand | — |
| D | Nuclear receptor coactivator 2 | protein | 8 | 75% helix, 0% strand | — |
Ligands and binding sites
- 7EM · 4,4',4''-(thiene-2,3,5-triyl)triphenol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.86 | 0.95 | 35 | 7EM |
| 2 | 493 | 0.82 | 0.88 | 34 | 7EM |
| 3 | 86 | 0.66 | 0.91 | 16 | empty |
| 4 | 77 | 0.61 | 0.89 | 18 | empty |
| 5 | 135 | 0.58 | 0.83 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1610 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 458 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 387 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- P03372 · AlphaFold monomer V2.0 prediction for estrogen receptor (P03372) · a predicted model of the same protein · chain B against A, TM-score 0.98
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
- Elsewhere: RCSB PDB 5TLM · PDBe 5TLM · UniProt P03372
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