MolNFT v1 · #52368 · protein
The mbt repeats of human SCML2 bind to peptides containing mono methylated lysine.
2VYT · Sex comb on midleg-like protein 2: “The mbt repeats of human SCML2 bind to peptides containing mono methylated lysine.”. X-ray diffraction, 1 ligand (MLZ), 3 pockets (best druggability 0.37). MolNFT v1 #52368 on GenesisL1: 3D…
- 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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