Research workbench
Fab structure of anti-vaccinia virus D8L antigen mouse IGG2A LA5
Analyse Fab structure of anti-vaccinia virus D8L antigen mouse IGG2A LA5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EBQ
- Type
- protein
- Length
- 429 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-vaccinia D8L antigen monoclonal IGG2A antibody LA5, heavy chain; Anti-vaccinia D8L…
- Ligands
- CL, PO4
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Anti-vaccinia D8L antigen monoclonal IGG2A antibody LA5, heavy chain | protein | 218 | 8% helix, 52% strand | — |
| L | Anti-vaccinia D8L antigen monoclonal IGG2A antibody LA5, light chain | protein | 211 | 7% helix, 52% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains H
- PO4 · Phosphate ion · ion · chains H
- EDO · 1,2-ethanediol · additive · 2 copies · chains H, L
- GOL · Glycerol · additive · chains H, L
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 | 355 | 0.55 | 0.75 | 56 | EDO |
| 2 | 121 | 0.38 | 0.74 | 23 | empty |
| 3 | 62 | 0.36 | 0.78 | 17 | empty |
| 4 | 72 | 0.31 | 0.74 | 22 | empty |
| 5 | 51 | 0.27 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- H–L · 1934 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4EBQ · Fab structure of anti-Vaccinia virus D8L antigen mouse IgG2a LA5 · 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
- Elsewhere: RCSB PDB 4EBQ · PDBe 4EBQ
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