MolNFT v1 · #28426 · protein
Crystal structure of type-I restriction-modification system S subunit from M. genitalium
1YDX · Type I restriction enzyme specificity protein MG438: “Crystal structure of type-I restriction-modification system S subunit from M. genitalium”. X-ray diffraction, 1 ligand (CL), 4 pockets (best druggability 0.53). MolNFT v1 #28426…
- PDB
- 1YDX
- Type
- protein
- Length
- 374 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type I restriction enzyme specificity protein MG438
- UniProt
- Q49434
- Ligands
- CL
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type I restriction enzyme specificity protein MG438 | protein | 374 | 40% helix, 21% strand | Q49434 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.53 | 0.75 | 30 | empty |
| 2 | 190 | 0.46 | 0.74 | 31 | empty |
| 3 | 83 | 0.39 | 0.78 | 18 | empty |
| 4 | 57 | 0.34 | 0.77 | 12 | empty |
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 1YDX · Crystal structure of Type-I restriction-modification system S subunit from M. genitalium · the same entry in another collection · chain A against A, TM-score 1.00
- Q49434 · AlphaFold monomer V2.0 prediction for putative type-1 restriction enzyme specificity… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q49434
- Elsewhere: RCSB PDB 1YDX · PDBe 1YDX · UniProt Q49434
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