Research workbench
Crystal structure of human germline antibody IGHV3-23/IGKV1-39
Analyse Crystal structure of human germline antibody IGHV3-23/IGKV1-39 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I19
- Type
- protein
- Length
- 434 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab light chain; Fab heavy chain
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab light chain | protein | 213 | 6% helix, 50% strand | — |
| H | Fab heavy chain | protein | 221 | 10% helix, 51% strand | — |
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 | 516 | 0.60 | 0.74 | 51 | empty |
| 2 | 169 | 0.46 | 0.75 | 28 | empty |
| 3 | 105 | 0.39 | 0.76 | 19 | empty |
| 4 | 52 | 0.30 | 0.76 | 11 | empty |
| 5 | 56 | 0.27 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- L–H · 1924 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5I19 · Crystal structure of human germline antibody IGHV3-23/IGKV1-39 · 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 5I19 · PDBe 5I19
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