Research workbench
The M23 peptidase domain of the staphylococcal phage 2638A endolysin
Analyse The M23 peptidase domain of the staphylococcal phage 2638A endolysin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YJ1
- Type
- protein
- Length
- 338 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ORF007
- UniProt
- Q4ZD58
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ORF007 | protein | 169 | 11% helix, 34% strand | Q4ZD58 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 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 | 260 | 0.70 | 0.85 | 34 | empty |
| 2 | 272 | 0.69 | 0.84 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 158 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6YJ1 · The M23 peptidase domain of the Staphylococcal phage 2638A endolysin · 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 Q4ZD58
- Elsewhere: RCSB PDB 6YJ1 · PDBe 6YJ1 · UniProt Q4ZD58
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