Research workbench
Structure of alkaline D-peptidase from bacillus cereus
Analyse Structure of alkaline D-peptidase from bacillus cereus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y7P
- Type
- protein
- Length
- 342 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkaline D-peptidase
- UniProt
- P94288
- Ligands
- SCN
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alkaline D-peptidase | protein | 342 | 32% helix, 19% strand | P94288 |
Ligands and binding sites
- SCN · Thiocyanate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.65 | 0.78 | 44 | empty |
| 2 | 66 | 0.30 | 0.74 | 19 | empty |
Compared structures
- 4Y7P · Structure of alkaline D-peptidase from Bacillus cereus · the same entry in another collection · chain A against A, TM-score 1.00
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 P94288
- Elsewhere: RCSB PDB 4Y7P · PDBe 4Y7P · UniProt P94288
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