Research workbench
Crystal structure of the PRDM9 set domain in complex with H3K4ME2 and adohcy.
Analyse Crystal structure of the PRDM9 set domain in complex with H3K4ME2 and adohcy. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C1Q
- Type
- protein
- Length
- 342 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase PRDM9; Histone H3.1
- EC
- 2.1.1.43
- UniProt
- Q96EQ9, P68431
- Ligands
- SAH, ZN
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase PRDM9 (EC 2.1.1.43) | protein | 173 | 12% helix, 31% strand | Q96EQ9 |
| B | Histone-lysine N-methyltransferase PRDM9 (EC 2.1.1.43) | protein | 162 | 7% helix, 34% strand | Q96EQ9 |
| C | Histone H3.1 | protein | 7 | 0% helix, 29% strand | P68431 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 665 | 0.67 | 0.76 | 71 | SAH |
| 2 | 74 | 0.48 | 0.83 | 16 | empty |
| 3 | 156 | 0.45 | 0.76 | 26 | empty |
| 4 | 64 | 0.44 | 0.82 | 16 | empty |
| 5 | 78 | 0.38 | 0.77 | 15 | GOL |
Interfaces
2 interfaces between chains.
- A–C · 686 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 577 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 4C1Q · Crystal structure of the PRDM9 SET domain in complex with H3K4me2 and AdoHcy. · the same entry in another collection · chain A against A, TM-score 1.00
- Q96EQ9 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase PRDM9 (Q96EQ9) · a predicted model of the same protein · chain B against A, TM-score 0.97
- P68431 · AlphaFold monomer V2.0 prediction for histone H3.1 (P68431) · a predicted model of the same protein · chain C against A, TM-score 0.62
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 Q96EQ9
- Every structure of UniProt P68431
- Elsewhere: RCSB PDB 4C1Q · PDBe 4C1Q · UniProt Q96EQ9 · UniProt P68431
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