Research workbench
Human MSL3 chromodomain bound to DNA and H4K20ME1 peptide
Analyse Human MSL3 chromodomain bound to DNA and H4K20ME1 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OA6
- Type
- protein + DNA
- Length
- 237 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Male-specific lethal 3 homolog; DNA (5'-D(*GP*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*A)…
- UniProt
- Q8N5Y2
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Male-specific lethal 3 homolog | protein | 84 | 25% helix, 40% strand | Q8N5Y2 |
| C, E | DNA (5'-D(*GP*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*A)- 3') | dna | 16 | — | — |
| D, F | DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*AP*G)- 3') | dna | 16 | — | — |
| G | H4 peptide monomethylated at lysine 20 | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- IMD · Imidazole · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.56 | 0.74 | 35 | empty |
| 2 | 144 | 0.50 | 0.80 | 23 | empty |
| 3 | 190 | 0.47 | 0.75 | 24 | empty |
| 4 | 166 | 0.44 | 0.74 | 20 | IMD |
Interfaces
12 interfaces between chains.
- E–F · 672 Ų buried · 72 hydrogen bonds · nucleic-nucleic
- C–D · 671 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- A–G · 397 Ų buried · 2 hydrogen bonds · protein-protein
- B–F · 200 Ų buried · 4 hydrogen bonds · protein-nucleic
- B–D · 150 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
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 Q8N5Y2
- Elsewhere: RCSB PDB 3OA6 · PDBe 3OA6 · UniProt Q8N5Y2
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