Research workbench
Crystal structure of the four mbt repeats of drosophila melanogaster sfmbt in complex with peptide rhr (ME)K vlr
Analyse Crystal structure of the four mbt repeats of drosophila melanogaster sfmbt in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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