MolNFT v1 · #124855 · protein
Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with 4,4'-((5-bromo-2,3-dihydro-1H-inden-1-ylidene) METHYLENE)DIPHENOL
5KRK · Estrogen receptor: “Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with…”. X-ray diffraction, 1 ligand (6WQ), 7 pockets (best druggability 0.85). MolNFT v1 #124855 on GenesisL1: 3D structure, binding…
- PDB
- 5KRK
- Type
- protein
- Length
- 468 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; NCOA2
- UniProt
- P03372
- Ligands
- 6WQ
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 68% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 228 | 68% helix, 3% strand | P03372 |
| B | Estrogen receptor | protein | 221 | 67% helix, 4% strand | P03372 |
| C | NCOA2 | protein | 10 | 70% helix, 0% strand | — |
| D | NCOA2 | protein | 9 | 56% helix, 0% strand | — |
Ligands and binding sites
- 6WQ · 4-[(5-bromanyl-2,3-dihydroinden-1-ylidene)-(4-hydroxyphenyl)methyl]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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.85 | 0.97 | 28 | 6WQ |
| 2 | 276 | 0.81 | 0.92 | 34 | 6WQ |
| 3 | 88 | 0.66 | 0.91 | 17 | empty |
| 4 | 90 | 0.62 | 0.89 | 20 | empty |
| 5 | 167 | 0.54 | 0.80 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1719 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 497 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 459 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5KRK · 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 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 5KRK · PDBe 5KRK · UniProt P03372
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