MolNFT v1 · #135001 · protein
Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with octane-1,8-diyl BIS(2,3-BIS(4-HYDROXYPHENYL)PENTANOATE)
5TLT · Estrogen receptor: “Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with octane-1,8-diyl…”. X-ray diffraction, 1 ligand (7ED), 7 pockets (best druggability 0.83). MolNFT v1 #135001 on GenesisL1: 3D…
- PDB
- 5TLT
- 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
- Ligands
- 7ED
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 234 | 70% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 240 | 68% helix, 4% strand | P03372 |
| C | Nuclear receptor coactivator 2 | protein | 10 | 50% helix, 0% strand | — |
| D | Nuclear receptor coactivator 2 | protein | 9 | 78% helix, 0% strand | — |
Ligands and binding sites
- 7ED · 8-{[2,3-bis(4-hydroxyphenyl)pentanoyl]oxy}octyl (2R, 3S)-2,3-bis(4-hydroxyphenyl)pentanoate · 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 | 259 | 0.83 | 0.94 | 33 | 7ED |
| 2 | 304 | 0.83 | 0.93 | 30 | 7ED |
| 3 | 80 | 0.64 | 0.90 | 18 | empty |
| 4 | 89 | 0.64 | 0.90 | 17 | empty |
| 5 | 205 | 0.54 | 0.78 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1663 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 520 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 514 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5TLT · Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with… · 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 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 5TLT · PDBe 5TLT · UniProt P03372
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