Research workbench
Crystal structure of human set and mynd domain containing protein 2 with MTF9975
Analyse Crystal structure of human set and mynd domain containing protein 2 with MTF9975 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CBY
- Type
- protein
- Length
- 850 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
- EW4, ZN
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 52% 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 | 428 | 51% helix, 14% strand | Q9NRG4 |
| B | N-lysine methyltransferase SMYD2 (EC 2.1.1.-, 2.1.1.43) | protein | 422 | 52% helix, 13% strand | Q9NRG4 |
Ligands and binding sites
- EW4 · [3-(4-amino-6-methyl-1H-imidazo[4,5-c]pyridin-1-yl)-3-methylazetidin-1-yl][1-({1-[(1R)-cyclohept-2-en-1-yl]piperidin-4-yl}methyl)-1H-pyrrol-3-yl]methanone · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 903 | 0.78 | 0.80 | 86 | EW4 |
| 2 | 1098 | 0.77 | 0.79 | 101 | EW4 |
| 3 | 370 | 0.61 | 0.77 | 32 | empty |
| 4 | 179 | 0.45 | 0.74 | 18 | empty |
| 5 | 137 | 0.42 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 846 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6CBY · Crystal structure of human SET and MYND Domain Containing protein 2 with MTF9975 · 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 B 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 6CBY · PDBe 6CBY · UniProt Q9NRG4
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