Research workbench
Crystal structure of ATXR5 in complex with histone H3.1
Analyse Crystal structure of ATXR5 in complex with histone H3.1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VBC
- Type
- protein
- Length
- 458 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable histone-lysine N-methyltransferase ATXR5; Histone H3.1 peptide
- EC
- 2.1.1.43
- UniProt
- B9RU15, P59226
- Ligands
- SAH
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable histone-lysine N-methyltransferase ATXR5 (EC 2.1.1.43) | protein | 216 | 25% helix, 30% strand | B9RU15 |
| B | Probable histone-lysine N-methyltransferase ATXR5 (EC 2.1.1.43) | protein | 215 | 25% helix, 29% strand | B9RU15 |
| C | Histone H3.1 peptide | protein | 14 | 0% helix, 21% strand | P59226 |
| D | Histone H3.1 peptide | protein | 13 | 0% helix, 23% strand | P59226 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, C, B, D
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.65 | 0.87 | 23 | empty |
| 2 | 151 | 0.64 | 0.86 | 24 | DMS |
| 3 | 130 | 0.49 | 0.79 | 19 | SAH |
| 4 | 120 | 0.47 | 0.78 | 20 | SAH |
| 5 | 177 | 0.45 | 0.75 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1105 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1074 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 116 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 50 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5VBC · Crystal structure of ATXR5 in complex with histone H3.1 · the same entry in another collection · chain D against D, 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
- P59226 · AlphaFold monomer V2.0 prediction for histone H3.2 (P59226) · a predicted model of the same protein · chain D against A, TM-score 0.24
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 P59226
- Elsewhere: RCSB PDB 5VBC · PDBe 5VBC · UniProt B9RU15 · UniProt P59226
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