MolNFT v1 · #136986 · protein
Crystal structure of ATXR5 set domain in complex with K36ME3 histone H3 peptide
5VAC · Probable histone-lysine N-methyltransferase ATXR5: “Crystal structure of ATXR5 set domain in complex with K36ME3 histone H3 peptide”. X-ray diffraction, 1 ligand (SAH), 2 pockets (best druggability 0.64). MolNFT v1 #136986 on…
- 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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