MolNFT v1 · #96308 · protein
Structure of phosphotyrosine (ptyr) scaffold bound to ptyr peptide
4JFX · Fab light chain: “Structure of phosphotyrosine (ptyr) scaffold bound to ptyr peptide”. X-ray diffraction, 9 pockets (best druggability 0.59). MolNFT v1 #96308 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4JFX
- Type
- protein
- Length
- 880 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab light chain; Fab heavy chain; Phosphopeptide
- Pockets
- 9 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | Fab light chain | protein | 214 | 6% helix, 50% strand | — |
| B | Fab heavy chain | protein | 225 | 7% helix, 52% strand | — |
| H | Fab heavy chain | protein | 219 | 7% helix, 53% strand | — |
| P | Phosphopeptide | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B, L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 431 | 0.59 | 0.75 | 51 | PG4 |
| 2 | 337 | 0.55 | 0.75 | 44 | PG4 |
| 3 | 203 | 0.52 | 0.77 | 35 | empty |
| 4 | 239 | 0.48 | 0.74 | 25 | empty |
| 5 | 231 | 0.46 | 0.73 | 27 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1785 Ų buried · 12 hydrogen bonds · protein-protein
- L–H · 1677 Ų buried · 14 hydrogen bonds · protein-protein
- B–H · 635 Ų buried · 15 hydrogen bonds · protein-protein
- H–P · 479 Ų buried · 13 hydrogen bonds · protein-protein
- L–P · 193 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 1 modified (disulfide, phosphorylation).
Compared structures
- 4JFX · Structure of phosphotyrosine (pTyr) scaffold bound to pTyr peptide · 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
- Elsewhere: RCSB PDB 4JFX · PDBe 4JFX
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