Research workbench
Crystal structure of the tail sheath protein protease resistant fragment from bacteriophage phikz
Analyse Crystal structure of the tail sheath protein protease resistant fragment from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SPE
- Type
- protein
- Length
- 506 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PHIKZ029
- UniProt
- Q8SDD3
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PHIKZ029 | protein | 252 | 19% helix, 32% strand | Q8SDD3 |
| B | PHIKZ029 | protein | 254 | 18% helix, 33% strand | Q8SDD3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.38 | 0.79 | 19 | empty |
| 2 | 61 | 0.36 | 0.78 | 18 | empty |
| 3 | 59 | 0.32 | 0.76 | 15 | PO4 |
| 4 | 59 | 0.29 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1202 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 3SPE · Crystal structure of the tail sheath protein protease resistant fragment from… · 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 Q8SDD3
- Elsewhere: RCSB PDB 3SPE · PDBe 3SPE · UniProt Q8SDD3
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