Research workbench
Human IGA1 Fab fragment
Analyse Human IGA1 Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M8O
- Type
- protein
- Length
- 440 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin A1 light chain; Immunoglobulin A1 heavy chain
- Ligands
- CL
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Immunoglobulin A1 light chain | protein | 219 | 6% helix, 50% strand | — |
| H | Immunoglobulin A1 heavy chain | protein | 221 | 8% helix, 52% 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 | 497 | 0.62 | 0.76 | 59 | CL |
| 2 | 113 | 0.39 | 0.75 | 23 | CL |
| 3 | 118 | 0.36 | 0.73 | 24 | empty |
| 4 | 64 | 0.30 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- L–H · 1758 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3M8O · Human IgA1 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 3M8O · PDBe 3M8O
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