MolNFT v1 · #94718 · protein
Methyltransferase domain of human euchromatic histone methyltransferase 1, mutant Y1211A
4I51 · Histone-lysine N-methyltransferase EHMT1: “Methyltransferase domain of human euchromatic histone methyltransferase 1, mutant Y1211A”. X-ray diffraction, 3 ligands (SAH, ZN, UNX), 9 pockets (best druggability 0.81). MolNFT v1 #94718…
- PDB
- 4I51
- Type
- protein
- Length
- 545 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase EHMT1; H3K9 ne-allyl peptide; Unknown peptide
- EC
- 2.1.1.-, 2.1.1.43
- UniProt
- Q9H9B1
- Ligands
- SAH, ZN, UNX
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase EHMT1 (EC 2.1.1.-, 2.1.1.43) | protein | 261 | 10% helix, 26% strand | Q9H9B1 |
| C | H3K9 ne-allyl peptide | protein | 9 | 0% helix, 22% strand | — |
| B | Histone-lysine N-methyltransferase EHMT1 (EC 2.1.1.-, 2.1.1.43) | protein | 258 | 11% helix, 26% strand | Q9H9B1 |
| D | H3K9 ne-allyl peptide | protein | 7 | 0% helix, 14% strand | — |
| K | Unknown peptide | protein | 10 | 40% helix, 0% strand | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, C, B, D
- ZN · Zinc ion · metal · 8 copies · chains A, B
- UNX · Unknown atom or ion · ion · 9 copies · chains A, B
- GOL · Glycerol · additive · 3 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.81 | 0.83 | 95 | GOL, UNX |
| 2 | 268 | 0.62 | 0.80 | 34 | empty |
| 3 | 200 | 0.57 | 0.80 | 24 | SAH |
| 4 | 212 | 0.54 | 0.78 | 26 | SAH |
| 5 | 87 | 0.38 | 0.76 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1083 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 797 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 695 Ų buried · 15 hydrogen bonds · protein-protein
- B–K · 192 Ų buried · 2 hydrogen bonds · protein-protein
- A–K · 89 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 4I51 · Methyltransferase domain of HUMAN EUCHROMATIC HISTONE METHYLTRANSFERASE 1, mutant Y1211A · 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 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 Q9H9B1
- Elsewhere: RCSB PDB 4I51 · PDBe 4I51 · UniProt Q9H9B1
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