MolNFT v1 · #50342 · protein
Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with sah and dimethylated H3K9 peptide
2RFI · Histone-lysine N-methyltransferase, H3 lysine-9 specific 5: “Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with sah…”. X-ray diffraction, 2 ligands (SAH, ZN), 9 pockets (best…
- PDB
- 2RFI
- Type
- protein
- Length
- 527 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase, H3 lysine-9 specific 5; Histone H3
- EC
- 2.1.1.43
- UniProt
- Q9H9B1
- Ligands
- SAH, ZN
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase, H3 lysine-9 specific 5 (EC 2.1.1.43) | protein | 261 | 10% helix, 26% strand | Q9H9B1 |
| B | Histone-lysine N-methyltransferase, H3 lysine-9 specific 5 (EC 2.1.1.43) | protein | 252 | 11% helix, 25% strand | Q9H9B1 |
| P | Histone H3 | protein | 8 | 0% helix, 13% strand | — |
| Q | Histone H3 | protein | 6 | 0% helix, 17% strand | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, P, B, Q
- ZN · Zinc ion · metal · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.81 | 0.82 | 96 | empty |
| 2 | 213 | 0.56 | 0.79 | 25 | SAH |
| 3 | 196 | 0.56 | 0.79 | 23 | SAH |
| 4 | 114 | 0.42 | 0.77 | 22 | empty |
| 5 | 84 | 0.35 | 0.75 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1073 Ų buried · 18 hydrogen bonds · protein-protein
- A–P · 793 Ų buried · 22 hydrogen bonds · protein-protein
- B–Q · 698 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 2RFI · Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9H9B1 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase EHMT1 (Q9H9B1) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 Q9H9B1
- Elsewhere: RCSB PDB 2RFI · PDBe 2RFI · UniProt Q9H9B1
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