Research workbench
Crystal structure of the anti-human prostaglandin E receptor EP4 antibody Fab fragment
Analyse Crystal structure of the anti-human prostaglandin E receptor EP4 antibody Fab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YFI
- Type
- protein
- Length
- 435 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of Fab fragment; Heavy chain of Fab fragment
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Light chain of Fab fragment | protein | 214 | 7% helix, 53% strand | — |
| H | Heavy chain of Fab fragment | protein | 221 | 7% helix, 53% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.64 | 0.74 | 64 | empty |
| 2 | 182 | 0.48 | 0.76 | 24 | empty |
| 3 | 146 | 0.45 | 0.76 | 25 | empty |
| 4 | 96 | 0.33 | 0.73 | 20 | empty |
| 5 | 53 | 0.27 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- L–H · 1954 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5YFI · Crystal structure of the anti-human prostaglandin E receptor EP4 antibody Fab fragment · 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 5YFI · PDBe 5YFI
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