MolNFT v1 · #101818 · protein
Crystal structure of ATXR5 in complex with histone H3.1 and adohcy
4O30 · Histone-lysine N-methyltransferase ATXR6, putative: “Crystal structure of ATXR5 in complex with histone H3.1 and adohcy”. X-ray diffraction, 1 ligand (SAH), 5 pockets (best druggability 0.65). MolNFT v1 #101818 on GenesisL1: 3D…
- PDB
- 4O30
- Type
- protein
- Length
- 459 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase ATXR6, putative; Histone H3.1
- EC
- 2.1.1.43
- UniProt
- B9RU15
- Ligands
- SAH
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase ATXR6, putative (EC 2.1.1.43) | protein | 217 | 24% helix, 29% strand | B9RU15 |
| B | Histone-lysine N-methyltransferase ATXR6, putative (EC 2.1.1.43) | protein | 216 | 24% helix, 28% strand | B9RU15 |
| C | Histone H3.1 | protein | 14 | 0% helix, 14% strand | — |
| D | Histone H3.1 | protein | 12 | 0% helix, 25% strand | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, C, B, D
- DMS · Dimethyl sulfoxide · additive · chains A
- BME · Beta-mercaptoethanol · additive · chains B
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 | 140 | 0.65 | 0.87 | 22 | DMS |
| 2 | 155 | 0.64 | 0.86 | 26 | BME |
| 3 | 132 | 0.49 | 0.79 | 19 | SAH |
| 4 | 222 | 0.47 | 0.74 | 24 | empty |
| 5 | 114 | 0.47 | 0.79 | 19 | SAH |
Interfaces
3 interfaces between chains.
- A–C · 1066 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 1009 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 135 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4O30 · Crystal structure of ATXR5 in complex with histone H3.1 and AdoHcy · the same entry in another collection · chain B against B, 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
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
- Elsewhere: RCSB PDB 4O30 · PDBe 4O30 · UniProt B9RU15
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