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Crystal structure of a pesticin (translocation and receptor binding domain) from Y. pestis and T4-lysozyme chimera
Analyse Crystal structure of a pesticin (translocation and receptor binding domain)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ARJ
- Type
- protein
- Length
- 635 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pesticin, lysozyme
- EC
- 3.2.1.17
- UniProt
- Q57159, P00720
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pesticin, lysozyme (EC 3.2.1.17) | protein | 318 | 44% helix, 20% strand | Q57159, P00720 |
| B | Pesticin, lysozyme (EC 3.2.1.17) | protein | 317 | 44% helix, 21% strand | Q57159, P00720 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.50 | 0.80 | 22 | empty |
| 2 | 124 | 0.42 | 0.76 | 17 | empty |
| 3 | 127 | 0.38 | 0.74 | 22 | empty |
| 4 | 91 | 0.34 | 0.74 | 24 | empty |
| 5 | 65 | 0.30 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 238 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4ARJ · Crystal structure of a pesticin (translocation and receptor binding domain) from Y.… · 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 4ARJ · PDBe 4ARJ · UniProt Q57159 · UniProt P00720
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