Research workbench
Hexagonal complex structure of atrx add bound to H3K9ME3 peptide
Analyse Hexagonal complex structure of atrx add bound to H3K9ME3 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QLA
- Type
- protein
- Length
- 266 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator atrx; Peptide of histone H3.3
- EC
- 3.6.4.12
- UniProt
- P46100, P84243
- Ligands
- ZN, K
- Pockets
- 2 · best druggability 0.40
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator atrx (EC 3.6.4.12) | protein | 127 | 34% helix, 13% strand | P46100 |
| C, F | Peptide of histone H3.3 | protein | 10 | 0% helix, 30% strand | P84243 |
| D | Transcriptional regulator atrx (EC 3.6.4.12) | protein | 119 | 35% helix, 13% strand | P46100 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.40 | 0.77 | 20 | empty |
| 2 | 69 | 0.31 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 722 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 717 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 644 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 3QLA · Hexagonal complex structure of ATRX ADD bound to H3K9me3 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P46100 · AlphaFold monomer V2.0 prediction for transcriptional regulator atrx (P46100) · a predicted model of the same protein · chain D against A, TM-score 0.95
- P84243 · AlphaFold monomer V2.0 prediction for histone H3.3 (P84243) · a predicted model of the same protein · chain C against A, TM-score 0.42
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 P46100
- Every structure of UniProt P84243
- Elsewhere: RCSB PDB 3QLA · PDBe 3QLA · UniProt P46100 · UniProt P84243
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