MolNFT v1 · #124858 · protein
Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with the METHYL(PHENYL)AMINO-substituted estrogen, (8R,9S, 13S,14S,17S)-13-methyl-17-(METHYL(PHENYL)AMINO)-7,8,9,11,12,13,14,15, 16,17-decahydro-6H-CYCLOPENTA[A]PHENANTHREN-3-ol
5KRO · Estrogen receptor: “Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with the…”. X-ray diffraction, 1 ligand (6WW), 6 pockets (best druggability 0.84). MolNFT v1 #124858 on GenesisL1: 3D structure, binding…
- PDB
- 5KRO
- Type
- protein
- Length
- 475 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; NCOA2
- UniProt
- P03372
- Ligands
- 6WW
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 68% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 229 | 69% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 228 | 67% helix, 3% strand | P03372 |
| C, D | NCOA2 | protein | 9 | 78% helix, 0% strand | — |
Ligands and binding sites
- 6WW · (8~{R},9~{S},13~{S},14~{S},17~{S})-13-methyl-17-[methyl(phenyl)amino]-6,7,8,9,11,12,14,15,16,17-decahydrocyclopenta[a]phenanthren-3-ol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 193 | 0.84 | 0.97 | 24 | 6WW |
| 2 | 303 | 0.81 | 0.91 | 33 | 6WW |
| 3 | 86 | 0.62 | 0.89 | 17 | empty |
| 4 | 78 | 0.62 | 0.90 | 17 | empty |
| 5 | 240 | 0.55 | 0.77 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1738 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 514 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 513 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5KRO · Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with the… · 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
- Elsewhere: RCSB PDB 5KRO · PDBe 5KRO · UniProt P03372
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