Research workbench
Apo structure of phosphotyrosine (pyab) scaffold
Analyse Apo structure of phosphotyrosine (pyab) scaffold in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JFY
- Type
- protein
- Length
- 863 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab light chain; Fab heavy chain
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab light chain | protein | 211 | 4% helix, 50% strand | — |
| B | Fab heavy chain | protein | 214 | 6% helix, 51% strand | — |
| L | Fab light chain | protein | 213 | 6% helix, 50% strand | — |
| H | Fab heavy chain | protein | 225 | 9% helix, 50% strand | — |
Ligands and binding sites
- PG4 · Tetraethylene glycol · additive · 4 copies · chains A, B, L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.65 | 0.94 | 17 | empty |
| 2 | 537 | 0.60 | 0.74 | 65 | PG4 |
| 3 | 468 | 0.59 | 0.74 | 53 | PG4 |
| 4 | 384 | 0.57 | 0.75 | 67 | empty |
| 5 | 351 | 0.55 | 0.74 | 28 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1803 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1600 Ų buried · 11 hydrogen bonds · protein-protein
- B–H · 964 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4JFY · Apo structure of phosphotyrosine (pYAb) scaffold · 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 4JFY · PDBe 4JFY
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