Research workbench
PFA1 Fab fragment complexed with pyro-GLU3-a-beta (3-8)
Analyse PFA1 Fab fragment complexed with pyro-GLU3-a-beta (3-8) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EYS
- Type
- protein
- Length
- 439 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- If kappa light chain; PFA1 Fab heavy chain; Pyro-GLU3-a-beta (3-8) peptide
- UniProt
- A2NHM3
- Pockets
- 3 · best druggability 0.49
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | If kappa light chain | protein | 219 | 7% helix, 52% strand | A2NHM3 |
| H | PFA1 Fab heavy chain | protein | 215 | 7% helix, 49% strand | — |
| Q | Pyro-GLU3-a-beta (3-8) peptide | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.49 | 0.74 | 38 | empty |
| 2 | 60 | 0.29 | 0.74 | 17 | empty |
| 3 | 62 | 0.28 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1836 Ų buried · 14 hydrogen bonds · protein-protein
- H–Q · 334 Ų buried · 9 hydrogen bonds · protein-protein
- L–Q · 281 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 modified (disulfide, alkylation, cyclization).
Compared structures
- 3EYS · PFA1 Fab fragment complexed with pyro-Glu3-A-Beta (3-8) · 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
- Every structure of UniProt A2NHM3
- Elsewhere: RCSB PDB 3EYS · PDBe 3EYS · UniProt A2NHM3
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