Research workbench
Structural insights for MPP8 chromodomain interaction with histone H3 lysine 9
Analyse Structural insights for MPP8 chromodomain interaction with histone H3 lysine 9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QO2
- Type
- protein
- Length
- 295 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M-phase phosphoprotein 8; Histone H3 peptide
- UniProt
- Q99549
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 6 distinct chains · 26% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M-phase phosphoprotein 8 | protein | 61 | 30% helix, 41% strand | Q99549 |
| P, S | Histone H3 peptide | protein | 15 | 0% helix, 33% strand | — |
| B | M-phase phosphoprotein 8 | protein | 59 | 29% helix, 44% strand | Q99549 |
| Q | Histone H3 peptide | protein | 13 | 0% helix, 38% strand | — |
| C, D | M-phase phosphoprotein 8 | protein | 59 | 39% helix, 42% strand | Q99549 |
| R | Histone H3 peptide | protein | 14 | 0% helix, 36% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains C, P, D, S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.54 | 0.77 | 37 | empty |
| 2 | 163 | 0.48 | 0.77 | 36 | empty |
| 3 | 109 | 0.48 | 0.80 | 18 | empty |
Interfaces
13 interfaces between chains.
- D–S · 761 Ų buried · 22 hydrogen bonds · protein-protein
- A–P · 754 Ų buried · 19 hydrogen bonds · protein-protein
- C–R · 723 Ų buried · 15 hydrogen bonds · protein-protein
- B–Q · 696 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 524 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (methylation).
Compared structures
- 3QO2 · Structural insights for MPP8 chromodomain interaction with histone H3 lysine 9 · the same entry in another collection · chain S against S, TM-score 1.00
- Q99549 · AlphaFold monomer V2.0 prediction for M-phase phosphoprotein 8 (Q99549) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 Q99549
- Elsewhere: RCSB PDB 3QO2 · PDBe 3QO2 · UniProt Q99549
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