Research workbench
Structure of PHOSPHOSERINE/THREONINE (pstab) scaffold bound to pser peptide
Analyse Structure of PHOSPHOSERINE/THREONINE (pstab) scaffold bound to pser peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JG0
- Type
- protein
- Length
- 446 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab light chain; Fab heavy chain; Phosphopeptide
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab light chain | protein | 214 | 6% helix, 50% strand | — |
| H | Fab heavy chain | protein | 224 | 8% helix, 52% strand | — |
| P | Phosphopeptide | protein | 8 | 0% helix, 13% strand | — |
Ligands and binding sites
- PPI · Propanoic acid · additive · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.61 | 0.80 | 39 | empty |
| 2 | 238 | 0.49 | 0.74 | 38 | empty |
| 3 | 116 | 0.38 | 0.74 | 22 | empty |
| 4 | 97 | 0.35 | 0.74 | 25 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1832 Ų buried · 16 hydrogen bonds · protein-protein
- H–P · 413 Ų buried · 16 hydrogen bonds · protein-protein
- L–P · 217 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 modified (disulfide, phosphorylation).
Compared structures
- 4JG0 · Structure of phosphoserine/threonine (pSTAb) scaffold bound to pSer peptide · the same entry in another collection · chain L against L, 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
- Elsewhere: RCSB PDB 4JG0 · PDBe 4JG0
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