MolNFT v1 · #77244 · protein
Crystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9ME3 peptide
3R93: “Crystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9ME3 peptide”. X-ray diffraction, 1 ligand (UNX), 2 pockets (best druggability 0.69). MolNFT v1 #77244 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3R93
- Type
- protein
- Length
- 283 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M-phase phosphoprotein 8; H3K9ME3 peptide
- UniProt
- Q99549
- Ligands
- UNX
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | M-phase phosphoprotein 8 | protein | 58 | 36% helix, 43% strand | Q99549 |
| D | M-phase phosphoprotein 8 | protein | 59 | 36% helix, 42% strand | Q99549 |
| E, G, H | H3K9ME3 peptide | protein | 12 | 0% helix, 42% strand | — |
| F | H3K9ME3 peptide | protein | 14 | 0% helix, 21% strand | — |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 749 | 0.69 | 0.76 | 72 | empty |
| 2 | 78 | 0.36 | 0.76 | 19 | empty |
Interfaces
13 interfaces between chains.
- C–G · 651 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 649 Ų buried · 14 hydrogen bonds · protein-protein
- D–H · 648 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 614 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 562 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (methylation).
Compared structures
- 3R93 · Crystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9Me3… · the same entry in another collection · chain H against H, TM-score 1.00
- Q99549 · AlphaFold monomer V2.0 prediction for M-phase phosphoprotein 8 (Q99549) · a predicted model of the same protein · chain A 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 3R93 · PDBe 3R93 · UniProt Q99549
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