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Crystal structure of bacillus subtilis yxep protein (APC1829), a dinuclear metal binding peptidase from M20 family
Analyse Crystal structure of bacillus subtilis yxep protein (APC1829), a dinuclear… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YSJ
- Type
- protein
- Length
- 715 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein yxep
- EC
- 3.5.1.14
- UniProt
- P54955
- Ligands
- NI
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein yxep (EC 3.5.1.14) | protein | 359 | 35% helix, 26% strand | P54955 |
| B | Protein yxep (EC 3.5.1.14) | protein | 356 | 33% helix, 29% strand | P54955 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.59 | 0.77 | 42 | NI |
| 2 | 228 | 0.52 | 0.76 | 29 | NI |
Interfaces
1 interface between chains.
- A–B · 1106 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 1YSJ · Crystal Structure of Bacillus Subtilis YXEP Protein (APC1829), a Dinuclear Metal Binding… · the same entry in another collection · chain A against A, TM-score 1.00
- P54955 · AlphaFold monomer V2.0 prediction for N-acetylcysteine deacetylase (P54955) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P54955
- Elsewhere: RCSB PDB 1YSJ · PDBe 1YSJ · UniProt P54955
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