MolNFT v1 · #124340 · protein
Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with oxabicyclic heptene sulfonamide (obhs-N)
5KCC · Estrogen receptor: “Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with oxabicyclic heptene…”. X-ray diffraction, 1 ligand (OB1), 9 pockets (best druggability 0.85). MolNFT v1 #124340 on GenesisL1: 3D…
- PDB
- 5KCC
- Type
- protein
- Length
- 483 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; NCOA2
- UniProt
- P03372
- Ligands
- OB1
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 237 | 69% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 227 | 68% helix, 4% strand | P03372 |
| C | NCOA2 | protein | 10 | 70% helix, 0% strand | — |
| D | NCOA2 | protein | 9 | 56% helix, 0% strand | — |
Ligands and binding sites
- OB1 · (1S,2R,4S)-5,6-bis(4-hydroxyphenyl)-N-phenyl-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.85 | 0.97 | 27 | OB1 |
| 2 | 311 | 0.82 | 0.92 | 38 | OB1 |
| 3 | 94 | 0.66 | 0.91 | 19 | empty |
| 4 | 91 | 0.65 | 0.90 | 17 | empty |
| 5 | 208 | 0.54 | 0.78 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1636 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 514 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 513 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5KCC · 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 5KCC · PDBe 5KCC · UniProt P03372
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