Research workbench
The structure of the bacteriophage T4 cell-puncturing device
Analyse The structure of the bacteriophage T4 cell-puncturing device in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1K28
- Type
- protein
- Length
- 921 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tail-associated lysozyme; Baseplate structural protein GP27
- EC
- 3.2.1.17
- UniProt
- P16009, P17172
- Ligands
- K, PO4
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tail-associated lysozyme (EC 3.2.1.17) | protein | 557 | 22% helix, 15% strand | P16009 |
| D | Baseplate structural protein GP27 | protein | 364 | 17% helix, 35% strand | P17172 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 501 | 0.73 | 0.82 | 62 | empty |
| 2 | 444 | 0.70 | 0.81 | 44 | empty |
| 3 | 252 | 0.65 | 0.83 | 35 | empty |
| 4 | 188 | 0.52 | 0.77 | 22 | empty |
| 5 | 72 | 0.51 | 0.85 | 20 | empty |
Interfaces
1 interface between chains.
- A–D · 963 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 1K28 · The Structure of the Bacteriophage T4 Cell-Puncturing Device · 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 P16009
- Every structure of UniProt P17172
- Elsewhere: RCSB PDB 1K28 · PDBe 1K28 · UniProt P16009 · UniProt P17172
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