Research workbench
PFA1 Fab fragment complexed with Ror2(518-525)
Analyse PFA1 Fab fragment complexed with Ror2(518-525) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EYU
- Type
- protein
- Length
- 444 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.71
- Source
- Mus musculus; SYNTHETIC CONSTRUCT
- Molecule
- If kappa light chain; PFA1 Fab Heavy Chain; ROR2(518-525) peptide
- UniProt
- A2NHM3
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · resolution 2.71 · 3 distinct chains · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | If kappa light chain | protein | 219 | 7% helix, 50% strand | A2NHM3 |
| H | PFA1 Fab Heavy Chain | protein | 219 | 5% helix, 46% strand | — |
| Q | ROR2(518-525) peptide | protein | 6 | 0% helix, 0% strand | — |
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 | 286 | 0.50 | 0.73 | 37 | empty |
| 2 | 80 | 0.35 | 0.76 | 18 | empty |
| 3 | 80 | 0.33 | 0.74 | 18 | empty |
| 4 | 79 | 0.29 | 0.72 | 19 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1897 Ų buried · 19 hydrogen bonds · protein-protein
- H–Q · 351 Ų buried · 9 hydrogen bonds · protein-protein
- L–Q · 340 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 modified (disulfide, alkylation).
Compared structures
- 3EYU · PFA1 Fab fragment complexed with ROR2(518-525) · the same entry in another collection · chain H against H, 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
- Every structure of UniProt A2NHM3
- Elsewhere: RCSB PDB 3EYU · PDBe 3EYU · UniProt A2NHM3
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