MolNFT v1 · #135549 · protein
Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with the phenylamino-substituted estrogen, (8R,9S,13S,14S, 17S)-13-methyl-17-(phenylamino)-7,8,9,11,12,13,14,15,16,17-decahydro- 6H-CYCLOPENTA[A]PHENANTHREN-3-ol, without a coactivator peptide
5U2B · Estrogen receptor: “Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with the phenylamino-substituted…”. X-ray diffraction, 1 ligand (6WV), 20 pockets (best druggability 0.84). MolNFT v1 #135549 on…
- PDB
- 5U2B
- Type
- protein
- Length
- 1,386 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor
- UniProt
- P03372
- Ligands
- 6WV
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 68% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 242 | 70% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 228 | 66% helix, 1% strand | P03372 |
| C | Estrogen receptor | protein | 244 | 70% helix, 4% strand | P03372 |
| D | Estrogen receptor | protein | 226 | 67% helix, 4% strand | P03372 |
| E | Estrogen receptor | protein | 221 | 67% helix, 3% strand | P03372 |
| F | Estrogen receptor | protein | 225 | 70% helix, 4% strand | P03372 |
Ligands and binding sites
- 6WV · (8~{R},9~{S},13~{S},14~{S},17~{S})-13-methyl-17-phenylazanyl-6,7,8,9,11,12,14,15,16,17-decahydrocyclopenta[a]phenanthren-3-ol · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 249 | 0.84 | 0.96 | 28 | 6WV |
| 2 | 248 | 0.84 | 0.96 | 29 | 6WV |
| 3 | 263 | 0.83 | 0.94 | 31 | 6WV |
| 4 | 250 | 0.81 | 0.93 | 30 | 6WV |
| 5 | 293 | 0.80 | 0.90 | 30 | 6WV |
Interfaces
5 interfaces between chains.
- A–B · 1675 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1671 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1453 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 630 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 587 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5U2B · Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with the… · the same entry in another collection · chain F against F, TM-score 1.00
- P03372 · AlphaFold monomer V2.0 prediction for estrogen receptor (P03372) · a predicted model of the same protein · chain E 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
- Elsewhere: RCSB PDB 5U2B · PDBe 5U2B · UniProt P03372
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