Research workbench
Structure of the salmonella virulence effector sptp in complex with its secretion chaperone sicp
Analyse Structure of the salmonella virulence effector sptp in complex with its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JYO
- Type
- protein
- Length
- 726 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sicp; Protein tyrosine phosphatase sptp
- UniProt
- O85300, P74873
- Pockets
- 9 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Sicp | protein | 130 | 45% helix, 28% strand | O85300 |
| E | Protein tyrosine phosphatase sptp | protein | 102 | 51% helix, 12% strand | P74873 |
| F | Protein tyrosine phosphatase sptp | protein | 104 | 48% helix, 10% strand | P74873 |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.61 | 0.79 | 37 | empty |
| 2 | 243 | 0.60 | 0.80 | 32 | empty |
| 3 | 202 | 0.56 | 0.79 | 39 | empty |
| 4 | 202 | 0.49 | 0.76 | 35 | empty |
| 5 | 116 | 0.45 | 0.78 | 24 | empty |
Interfaces
9 interfaces between chains.
- D–E · 1627 Ų buried · 18 hydrogen bonds · protein-protein
- C–F · 1616 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1180 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1170 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 1120 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1JYO · Structure of the Salmonella Virulence Effector SptP in Complex with its Secretion… · the same entry in another collection · chain F against F, TM-score 1.00
- P74873 · AlphaFold monomer V2.0 prediction for secreted effector protein sptp (P74873) · a predicted model of the same protein · chain F against A, TM-score 0.41
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 O85300
- Every structure of UniProt P74873
- Elsewhere: RCSB PDB 1JYO · PDBe 1JYO · UniProt O85300 · UniProt P74873
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