Research workbench
The mbt repeats of human SCML2 bind to peptides containing mono methylated lysine.
Analyse The mbt repeats of human SCML2 bind to peptides containing mono methylated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VYT
- Type
- protein
- Length
- 397 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sex comb on midleg-like protein 2
- UniProt
- Q9UQR0
- Ligands
- MLZ
- Pockets
- 3 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sex comb on midleg-like protein 2 | protein | 214 | 18% helix, 33% strand | Q9UQR0 |
| B | Sex comb on midleg-like protein 2 | protein | 183 | 15% helix, 31% strand | Q9UQR0 |
Ligands and binding sites
- MLZ · N-methyl-lysine · ligand · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.37 | 0.77 | 13 | empty |
| 2 | 57 | 0.28 | 0.74 | 15 | empty |
| 3 | 53 | 0.27 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 585 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2VYT · The MBT repeats of human SCML2 bind to peptides containing mono methylated lysine. · the same entry in another collection · chain B against B, TM-score 1.00
- Q9UQR0 · AlphaFold monomer V2.0 prediction for sex comb on midleg-like protein 2 (Q9UQR0) · 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 Q9UQR0
- Elsewhere: RCSB PDB 2VYT · PDBe 2VYT · UniProt Q9UQR0
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