MolNFT v1 · #96312 · protein
Structure of PHOSPHOSERINE/THREONINE (pstab) scaffold bound to pthr peptide
4JG1 · Fab light chain: “Structure of PHOSPHOSERINE/THREONINE (pstab) scaffold bound to pthr peptide”. X-ray diffraction, 4 pockets (best druggability 0.62). MolNFT v1 #96312 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4JG1
- Type
- protein
- Length
- 448 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 0.62
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab light chain | protein | 214 | 5% helix, 50% strand | — |
| H | Fab heavy chain | protein | 225 | 8% helix, 52% strand | — |
| P | Phosphopeptide | protein | 9 | 0% helix, 11% strand | — |
Ligands and binding sites
- PPI · Propanoic acid · additive · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 264 | 0.62 | 0.80 | 39 | PPI |
| 2 | 315 | 0.52 | 0.74 | 47 | empty |
| 3 | 115 | 0.38 | 0.74 | 21 | empty |
| 4 | 82 | 0.32 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1816 Ų buried · 15 hydrogen bonds · protein-protein
- H–P · 420 Ų buried · 17 hydrogen bonds · protein-protein
- L–P · 207 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 modified (disulfide, phosphorylation).
Compared structures
- 4JG1 · Structure of phosphoserine/threonine (pSTAb) scaffold bound to pThr 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 4JG1 · PDBe 4JG1
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