Research workbench
Crystal structure of methyltransferase domain of human pr domain- containing protein 9
Analyse Crystal structure of methyltransferase domain of human pr domain- containing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IJD
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase PRDM9
- EC
- 2.1.1.43
- UniProt
- Q9NQV7
- Ligands
- ZN, UNX
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase PRDM9 (EC 2.1.1.43) | protein | 215 | 17% helix, 29% strand | Q9NQV7 |
| B | Histone-lysine N-methyltransferase PRDM9 (EC 2.1.1.43) | protein | 215 | 19% helix, 27% strand | Q9NQV7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- UNX · Unknown atom or ion · ion · 24 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.75 | 0.78 | 99 | UNX |
| 2 | 111 | 0.41 | 0.76 | 24 | empty |
| 3 | 98 | 0.41 | 0.77 | 24 | UNX |
| 4 | 54 | 0.31 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 262 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 4IJD · Crystal structure of methyltransferase domain of human PR domain-containing protein 9 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NQV7 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase PRDM9 (Q9NQV7) · a predicted model of the same protein · chain B 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 Q9NQV7
- Elsewhere: RCSB PDB 4IJD · PDBe 4IJD · UniProt Q9NQV7
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