Research workbench
TR1.9 Fab fragment of a human IGG1 kappa autoantibody
Analyse TR1.9 Fab fragment of a human IGG1 kappa autoantibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VGE
- Type
- protein
- Length
- 439 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TR1.9 Fab
- UniProt
- P01857
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | TR1.9 Fab | protein | 214 | 6% helix, 50% strand | — |
| H | TR1.9 Fab | protein | 225 | 8% helix, 48% strand | P01857 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.57 | 0.90 | 22 | empty |
| 2 | 316 | 0.50 | 0.73 | 36 | empty |
| 3 | 102 | 0.41 | 0.77 | 21 | empty |
| 4 | 151 | 0.39 | 0.73 | 18 | empty |
| 5 | 60 | 0.36 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- L–H · 1977 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1VGE · TR1.9 Fab fragment of a human IGG1 kappa autoantibody · 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
- Every structure of UniProt P01857
- Elsewhere: RCSB PDB 1VGE · PDBe 1VGE · UniProt P01857
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