Research workbench
Structural basis of estrogen receptor alpha methylation mediated by histone methyltransferase SMYD2
Analyse Structural basis of estrogen receptor alpha methylation mediated by histone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O6F
- Type
- protein
- Length
- 440 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-lysine methyltransferase SMYD2; Estrogen receptor
- EC
- 2.1.1.-, 2.1.1.43
- UniProt
- Q9NRG4, P03372
- Ligands
- SAH, ZN, NI
- Pockets
- 8 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-lysine methyltransferase SMYD2 (EC 2.1.1.-, 2.1.1.43) | protein | 430 | 50% helix, 14% strand | Q9NRG4 |
| B | Estrogen receptor | protein | 10 | 0% helix, 10% strand | P03372 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A, B
- ZN · Zinc ion · metal · 3 copies · chains A
- NI · Nickel (II) ion · metal · 2 copies · chains A
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.64 | 0.81 | 33 | PE8 |
| 2 | 439 | 0.64 | 0.77 | 38 | empty |
| 3 | 97 | 0.63 | 0.89 | 28 | NI |
| 4 | 174 | 0.60 | 0.83 | 26 | SAH |
| 5 | 138 | 0.56 | 0.82 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1019 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4O6F · Structural Basis of Estrogen Receptor Alpha Methylation Mediated by Histone… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NRG4 · AlphaFold monomer V2.0 prediction for N-lysine methyltransferase SMYD2 (Q9NRG4) · a predicted model of the same protein · 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 B against A, TM-score 0.35
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 Q9NRG4
- Every structure of UniProt P03372
- Elsewhere: RCSB PDB 4O6F · PDBe 4O6F · UniProt Q9NRG4 · UniProt P03372
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