Research workbench
Crystal structure of histone lysine methyltransferase SMYD2 in complex with polyethylene glycol
Analyse Crystal structure of histone lysine methyltransferase SMYD2 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N3G
- Type
- protein
- Length
- 430 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-lysine methyltransferase SMYD2
- EC
- 2.1.1.-, 2.1.1.43
- UniProt
- Q9NRG4
- Ligands
- SAH, ZN, NI
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 50% 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 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
- NI · Nickel (II) ion · metal · 2 copies · chains A
- EOH · Ethanol · additive · 5 copies · chains A
- 12P · Dodecaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.80 | 0.81 | 103 | SAH, 12P, NI, EOH |
| 2 | 89 | 0.38 | 0.76 | 17 | empty |
| 3 | 55 | 0.36 | 0.79 | 15 | empty |
Compared structures
- 6N3G · Crystal structure of histone lysine methyltransferase SmyD2 in complex with polyethylene… · 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
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
- Elsewhere: RCSB PDB 6N3G · PDBe 6N3G · UniProt Q9NRG4
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