Research workbench
A histone H3K9M mutation traps histone methyltransferase CLR4 to prevent heterochromatin spreading
Analyse A histone H3K9M mutation traps histone methyltransferase CLR4 to prevent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T0M
- Type
- protein
- Length
- 549 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase EHMT2; Thr-lys-gln-thr-ala-arg-nle-ser-thr-gly
- EC
- 2.1.1.-, 2.1.1.43
- UniProt
- Q96KQ7
- Ligands
- SAM, SAH, ZN
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase EHMT2 (EC 2.1.1.-, 2.1.1.43) | protein | 260 | 12% helix, 25% strand | Q96KQ7 |
| P, C | Thr-lys-gln-thr-ala-arg-nle-ser-thr-gly | protein | 9 | 0% helix, 11% strand | — |
| B | Histone-lysine N-methyltransferase EHMT2 (EC 2.1.1.-, 2.1.1.43) | protein | 271 | 12% helix, 25% strand | Q96KQ7 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B, C
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- 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 | 1073 | 0.80 | 0.82 | 72 | empty |
| 2 | 188 | 0.54 | 0.78 | 23 | SAM |
| 3 | 180 | 0.53 | 0.79 | 22 | SAM, SAH |
| 4 | 72 | 0.43 | 0.81 | 21 | empty |
| 5 | 111 | 0.42 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1167 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 841 Ų buried · 21 hydrogen bonds · protein-protein
- A–P · 737 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 5T0M · A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin… · the same entry in another collection · chain C against C, TM-score 1.00
- Q96KQ7 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase EHMT2 (Q96KQ7) · 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 Q96KQ7
- Elsewhere: RCSB PDB 5T0M · PDBe 5T0M · UniProt Q96KQ7
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