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Co-crystal structure of human SMYD3 with a MEKK2 peptide at 2.13A
Analyse Co-crystal structure of human SMYD3 with a MEKK2 peptide at 2.13A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HQ8
- Type
- protein
- Length
- 870 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase SMYD3; MEKK2 peptide
- EC
- 2.1.1.43
- UniProt
- Q9H7B4
- Ligands
- SAH, ZN, MG
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 4 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 | 426 | 51% helix, 13% strand | Q9H7B4 |
| B | Histone-lysine N-methyltransferase SMYD3 (EC 2.1.1.43) | protein | 425 | 51% helix, 13% strand | Q9H7B4 |
| I | MEKK2 peptide | protein | 10 | 0% helix, 10% strand | — |
| J | MEKK2 peptide | protein | 9 | 0% helix, 11% strand | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, I, B, J
- ZN · Zinc ion · metal · 6 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, I, B, J
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.80 | 0.82 | 90 | EDO, SAH |
| 2 | 161 | 0.73 | 0.91 | 37 | EDO |
| 3 | 673 | 0.72 | 0.78 | 55 | EDO |
| 4 | 667 | 0.71 | 0.78 | 62 | EDO |
| 5 | 177 | 0.58 | 0.81 | 24 | SAH |
Interfaces
3 interfaces between chains.
- A–I · 948 Ų buried · 11 hydrogen bonds · protein-protein
- B–J · 770 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 368 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5HQ8 · Co-crystal Structure of human SMYD3 with a MEKK2 peptide at 2.13A · the same entry in another collection · chain B against B, 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 0.99
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 Q9H7B4
- Elsewhere: RCSB PDB 5HQ8 · PDBe 5HQ8 · UniProt Q9H7B4
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