MolNFT v1 · #157106 · protein
Crystal structure of human SMYD2 in complex with nle-peptide inhibitor
6MON · N-lysine methyltransferase SMYD2: “Crystal structure of human SMYD2 in complex with nle-peptide inhibitor”. X-ray diffraction, 2 ligands (SAH, ZN), 12 pockets (best druggability 0.81). MolNFT v1 #157106 on GenesisL1: 3D structure…
- PDB
- 6MON
- Type
- protein
- Length
- 870 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-lysine methyltransferase SMYD2; Lys-leu-nle-ser-lys-arg-gly
- EC
- 2.1.1.-, 2.1.1.43
- UniProt
- Q9NRG4
- Ligands
- SAH, ZN
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N-lysine methyltransferase SMYD2 (EC 2.1.1.-, 2.1.1.43) | protein | 429 | 51% helix, 14% strand | Q9NRG4 |
| C | Lys-leu-nle-ser-lys-arg-gly | protein | 5 | 0% helix, 20% strand | — |
| D | Lys-leu-nle-ser-lys-arg-gly | protein | 7 | 0% helix, 14% strand | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.81 | 0.82 | 117 | SAH |
| 2 | 769 | 0.69 | 0.76 | 70 | empty |
| 3 | 522 | 0.68 | 0.78 | 58 | empty |
| 4 | 82 | 0.65 | 0.91 | 27 | empty |
| 5 | 160 | 0.60 | 0.83 | 27 | SAH |
Interfaces
3 interfaces between chains.
- B–D · 730 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 665 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 568 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 6MON · Crystal structure of human SMYD2 in complex with Nle-peptide inhibitor · the same entry in another collection · chain D against D, 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 6MON · PDBe 6MON · UniProt Q9NRG4
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