Research workbench
Crystal structure of a conformation-dependent rabbit IgG Fab specific for amyloid prefibrillar oligomers
Analyse Crystal structure of a conformation-dependent rabbit IgG Fab specific for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HBC
- Type
- protein
- Length
- 423 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen binding fragment, immunoglobulin IgG - heavy chain; Antigen binding fragment…
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Antigen binding fragment, immunoglobulin IgG - heavy chain | protein | 210 | 6% helix, 51% strand | — |
| L | Antigen binding fragment, immunoglobulin IgG - light chain | protein | 213 | 7% helix, 53% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 523 | 0.61 | 0.75 | 55 | empty |
| 2 | 75 | 0.40 | 0.79 | 17 | empty |
| 3 | 77 | 0.34 | 0.75 | 20 | empty |
| 4 | 56 | 0.28 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- H–L · 1826 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 4HBC · Crystal structure of a conformation-dependent rabbit IgG Fab specific for amyloid… · 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 4HBC · PDBe 4HBC
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