MolNFT v1 · #118275 · protein
Crystal structure of human SMYD3 in complex with a VEGFR1 peptide
5EX3 · Histone-lysine N-methyltransferase SMYD3: “Crystal structure of human SMYD3 in complex with a VEGFR1 peptide”. X-ray diffraction, 2 ligands (SAH, ZN), 7 pockets (best druggability 0.75). MolNFT v1 #118275 on GenesisL1: 3D structure…
- PDB
- 5EX3
- Type
- protein
- Length
- 435 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase SMYD3; VEGFR1 peptide
- EC
- 2.1.1.43
- UniProt
- Q9H7B4
- Ligands
- SAH, ZN
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase SMYD3 (EC 2.1.1.43) | protein | 428 | 51% helix, 13% strand | Q9H7B4 |
| D | VEGFR1 peptide | protein | 7 | 0% helix, 14% strand | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A, D
- ZN · Zinc ion · metal · 3 copies · chains A
- ACY · Acetic acid · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.75 | 0.81 | 59 | empty |
| 2 | 81 | 0.61 | 0.89 | 26 | empty |
| 3 | 177 | 0.57 | 0.81 | 25 | SAH |
| 4 | 115 | 0.43 | 0.76 | 15 | empty |
| 5 | 103 | 0.38 | 0.75 | 29 | empty |
Interfaces
1 interface between chains.
- A–D · 706 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 5EX3 · Crystal structure of human SMYD3 in complex with a VEGFR1 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H7B4 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase SMYD3 (Q9H7B4) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9H7B4
- Elsewhere: RCSB PDB 5EX3 · PDBe 5EX3 · UniProt Q9H7B4
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