MolNFT v1 · #79873 · protein
Structure of SMYD2 in complex with P53 and sah
3TG5 · N-lysine methyltransferase SMYD2: “Structure of SMYD2 in complex with P53 and sah”. X-ray diffraction, 2 ligands (SAH, ZN), 5 pockets (best druggability 0.74). MolNFT v1 #79873 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3TG5
- Type
- protein
- Length
- 433 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-lysine methyltransferase SMYD2; Cellular tumor antigen P53
- EC
- 2.1.1.-, 2.1.1.43
- UniProt
- Q9NRG4, P04637
- Ligands
- SAH, ZN
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 48% 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 | 425 | 49% helix, 14% strand | Q9NRG4 |
| B | Cellular tumor antigen P53 | protein | 8 | 0% helix, 13% strand | P04637 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A, B
- ZN · Zinc ion · metal · 3 copies · chains A
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 920 | 0.74 | 0.78 | 73 | empty |
| 2 | 114 | 0.70 | 0.92 | 32 | GOL |
| 3 | 194 | 0.61 | 0.82 | 33 | SAH |
| 4 | 83 | 0.39 | 0.78 | 21 | empty |
| 5 | 88 | 0.38 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 875 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3TG5 · Structure of SMYD2 in complex with p53 and SAH · 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
- P04637 · AlphaFold monomer V2.0 prediction for cellular tumor antigen P53 (P04637) · a predicted model of the same protein · chain B against A, TM-score 0.49
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 P04637
- Elsewhere: RCSB PDB 3TG5 · PDBe 3TG5 · UniProt Q9NRG4 · UniProt P04637
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