Research workbench
Crystal structure of hera-lbd (Y537S) in complex with biochanin a
Analyse Crystal structure of hera-lbd (Y537S) in complex with biochanin a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JMM
- Type
- protein
- Length
- 485 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; Nuclear receptor coactivator 1
- EC
- 2.3.1.48
- UniProt
- P03372, Q15788
- Ligands
- QSO
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 231 | 71% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 235 | 67% helix, 3% strand | P03372 |
| F | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 9 | 78% helix, 0% strand | Q15788 |
| G | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 10 | 60% helix, 0% strand | Q15788 |
Ligands and binding sites
- QSO · 5,7-dihydroxy-3-(4-methoxyphenyl)-4H-chromen-4-one · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains B
- EDO · 1,2-ethanediol · additive · chains 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 | 164 | 0.82 | 0.97 | 25 | QSO |
| 2 | 253 | 0.76 | 0.89 | 31 | QSO |
| 3 | 92 | 0.65 | 0.90 | 19 | empty |
| 4 | 85 | 0.63 | 0.90 | 17 | empty |
| 5 | 191 | 0.51 | 0.77 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1686 Ų buried · 31 hydrogen bonds · protein-protein
- B–G · 525 Ų buried · 3 hydrogen bonds · protein-protein
- A–F · 505 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (oxidation).
Compared structures
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
- Every structure of UniProt Q15788
- Elsewhere: RCSB PDB 5JMM · PDBe 5JMM · UniProt P03372 · UniProt Q15788
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