Research workbench
The crystal structure of an engineered phage lysin containing the binding domain of pesticin and the killing domain of T4-lysozyme
Analyse The crystal structure of an engineered phage lysin containing the binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EXM
- Type
- protein
- Length
- 1,244 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pesticin, lysozyme chimera
- EC
- 3.2.1.17
- UniProt
- Q57159, P00720
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pesticin, lysozyme chimera (EC 3.2.1.17) | protein | 291 | 40% helix, 22% strand | Q57159, P00720 |
| B | Pesticin, lysozyme chimera (EC 3.2.1.17) | protein | 291 | 40% helix, 21% strand | Q57159, P00720 |
| C, D | Pesticin, lysozyme chimera (EC 3.2.1.17) | protein | 331 | 40% helix, 21% strand | Q57159, P00720 |
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.73 | 0.98 | 19 | empty |
| 2 | 535 | 0.70 | 0.79 | 74 | empty |
| 3 | 367 | 0.67 | 0.80 | 49 | empty |
| 4 | 504 | 0.65 | 0.77 | 50 | empty |
| 5 | 299 | 0.61 | 0.79 | 29 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1469 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 1462 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 663 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 413 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 181 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4EXM · The crystal structure of an engineered phage lysin containing the binding domain of… · 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 Q57159
- Every structure of UniProt P00720
- Elsewhere: RCSB PDB 4EXM · PDBe 4EXM · UniProt Q57159 · UniProt P00720
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