MolNFT v1 · #65778 · protein
Crystal structure of the four mbt repeats of drosophila melanogaster sfmbt in complex with peptide rhr (ME)K vlr
3H6Z · Polycomb protein sfmbt: “Crystal structure of the four mbt repeats of drosophila melanogaster sfmbt in complex with peptide rhr (ME)K…”. X-ray diffraction, 2 ligands (GLC, FRU), 9 pockets (best druggability 0.83). MolNFT v1 #65778…
- PDB
- 3H6Z
- Type
- protein
- Length
- 874 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polycomb protein sfmbt; 'HR(MLZ)VLR
- UniProt
- Q9VK33
- Ligands
- GLC, FRU
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Polycomb protein sfmbt | protein | 431 | 19% helix, 28% strand | Q9VK33 |
| L, M | 'HR(MLZ)VLR | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- FRU · beta-D-fructofuranose · sugar · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 572 | 0.83 | 0.88 | 62 | GLC, FRU |
| 2 | 587 | 0.82 | 0.87 | 66 | GLC, FRU |
| 3 | 197 | 0.68 | 0.87 | 27 | empty |
| 4 | 92 | 0.52 | 0.83 | 20 | empty |
| 5 | 98 | 0.50 | 0.82 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1028 Ų buried · 4 hydrogen bonds · protein-protein
- B–M · 455 Ų buried · 4 hydrogen bonds · protein-protein
- A–L · 449 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 3H6Z · Crystal Structure of the Four MBT Repeats of Drosophila melanogaster Sfmbt in Complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9VK33 · AlphaFold monomer V2.0 prediction for polycomb protein sfmbt (Q9VK33) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9VK33
- Elsewhere: RCSB PDB 3H6Z · PDBe 3H6Z · UniProt Q9VK33
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