Research workbench
Crystal structure of SHP2_SH2-caga EPIYA_D peptide complex
Analyse Crystal structure of SHP2_SH2-caga EPIYA_D peptide complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X94
- Type
- protein
- Length
- 449 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein phosphatase non-receptor type 11; Cag pathogenicity island protein
- EC
- 3.1.3.48
- UniProt
- Q06124, E6NP29
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 6 distinct chains · 18% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) | protein | 206 | 19% helix, 32% strand | Q06124 |
| B | Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) | protein | 207 | 19% helix, 30% strand | Q06124 |
| L | Cag pathogenicity island protein | protein | 9 | 0% helix, 33% strand | E6NP29 |
| M | Cag pathogenicity island protein | protein | 7 | 0% helix, 29% strand | E6NP29 |
| N | Cag pathogenicity island protein | protein | 13 | 0% helix, 15% strand | E6NP29 |
| O | Cag pathogenicity island protein | protein | 7 | 0% helix, 14% strand | E6NP29 |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 167 | 0.47 | 0.76 | 25 | empty |
| 2 | 167 | 0.46 | 0.75 | 29 | empty |
Interfaces
5 interfaces between chains.
- A–N · 664 Ų buried · 10 hydrogen bonds · protein-protein
- A–L · 591 Ų buried · 10 hydrogen bonds · protein-protein
- B–M · 556 Ų buried · 10 hydrogen bonds · protein-protein
- B–O · 495 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 194 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered, phosphorylation).
Compared structures
- 5X94 · Crystal structure of SHP2_SH2-CagA EPIYA_D peptide complex · 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 Q06124
- Every structure of UniProt E6NP29
- Elsewhere: RCSB PDB 5X94 · PDBe 5X94 · UniProt Q06124 · UniProt E6NP29
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