Research workbench
NMR structure of the type III secretory domain of yersinia yoph complexed with the skap-hom phospho-peptide N-acetyl-depyddpf-NH2
Analyse NMR structure of the type III secretory domain of yersinia yoph complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1M0V
- Type
- protein
- Length
- 137 residues
- Chains
- 2
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-tyrosine phosphatase yoph; SKAP55 homologue
- EC
- 3.1.3.48
- UniProt
- P08538
- Ligands
- ACE, NH2
- Pockets
- 1 · best druggability 0.36
Structure
solution nmr · 2 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein-tyrosine phosphatase yoph (EC 3.1.3.48) | protein | 130 | 44% helix, 15% strand | P08538 |
| B | SKAP55 homologue | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.36 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 375 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, phosphorylation).
Compared structures
- 1M0V · NMR STRUCTURE OF THE TYPE III SECRETORY DOMAIN OF YERSINIA YOPH COMPLEXED WITH THE… · the same entry in another collection · chain A against A, TM-score 1.00
- P08538 · AlphaFold monomer V2.0 prediction for tyrosine-protein phosphatase yoph (P08538) · a predicted model of the same protein · chain A against A, TM-score 0.69
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 P08538
- Elsewhere: RCSB PDB 1M0V · PDBe 1M0V · UniProt P08538
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