Research workbench
Human lysine methyltransferase SMYD2 in complex with adohcy
Analyse Human lysine methyltransferase SMYD2 in complex with adohcy in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RIB
- Type
- protein
- Length
- 848 residues
- Chains
- 2
- 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, SO4
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 51% 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 | 51% helix, 14% strand | Q9NRG4 |
| B | N-lysine methyltransferase SMYD2 (EC 2.1.1.-, 2.1.1.43) | protein | 418 | 51% helix, 13% strand | Q9NRG4 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 9 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.81 | 0.82 | 99 | SAH |
| 2 | 1015 | 0.80 | 0.81 | 109 | SAH, SO4 |
| 3 | 462 | 0.59 | 0.74 | 39 | empty |
| 4 | 188 | 0.56 | 0.79 | 23 | empty |
| 5 | 116 | 0.43 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 392 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3RIB · Human lysine methyltransferase Smyd2 in complex with AdoHcy · the same entry in another collection · chain B against B, 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 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 Q9NRG4
- Elsewhere: RCSB PDB 3RIB · PDBe 3RIB · UniProt Q9NRG4
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