Research workbench
Fab fragment of antiporphrin antibody 13G10
Analyse Fab fragment of antiporphrin antibody 13G10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AMK
- Type
- protein
- Length
- 425 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAB13G10, heavy chain; FAB13G10, light chain
- Ligands
- MG
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | FAB13G10, heavy chain | protein | 215 | 6% helix, 50% strand | — |
| L | FAB13G10, light chain | protein | 210 | 6% helix, 55% strand | — |
Ligands and binding sites
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 | 403 | 0.56 | 0.74 | 42 | empty |
| 2 | 134 | 0.46 | 0.77 | 22 | empty |
| 3 | 88 | 0.46 | 0.81 | 23 | GOL |
| 4 | 52 | 0.27 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- H–L · 1895 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4AMK · Fab fragment of antiporphrin antibody 13g10 · 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 4AMK · PDBe 4AMK
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.