Research workbench
Crystal structure of ATXR5 set domain in complex with K36ME3 histone H3 peptide
Analyse Crystal structure of ATXR5 set domain in complex with K36ME3 histone H3 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VAC
- Type
- protein
- Length
- 227 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable histone-lysine N-methyltransferase ATXR5; Histone H3.2
- EC
- 2.1.1.43
- UniProt
- B9RU15, Q71DI3
- Ligands
- SAH
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable histone-lysine N-methyltransferase ATXR5 (EC 2.1.1.43) | protein | 215 | 25% helix, 30% strand | B9RU15 |
| C | Histone H3.2 | protein | 12 | 0% helix, 25% strand | Q71DI3 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A, C
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.64 | 0.88 | 25 | DMS |
| 2 | 119 | 0.46 | 0.78 | 19 | SAH |
Interfaces
1 interface between chains.
- A–C · 1007 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5VAC · Crystal Structure of ATXR5 SET domain in complex with K36me3 histone H3 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- B9RU15 · AlphaFold monomer V2.0 prediction for probable histone-lysine N-methyltransferase ATXR5… · a predicted model of the same protein · chain A against A, TM-score 1.00
- Q71DI3 · AlphaFold monomer V2.0 prediction for histone H3.2 (Q71DI3) · a predicted model of the same protein · chain C against A, TM-score 0.28
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 B9RU15
- Every structure of UniProt Q71DI3
- Elsewhere: RCSB PDB 5VAC · PDBe 5VAC · UniProt B9RU15 · UniProt Q71DI3
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