Research workbench
Antibody Fab fragment
Analyse Antibody Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JQD
- Type
- protein
- Length
- 851 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D80 Fab fragment light chain; D80 Fab fragment heavy chain
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D80 Fab fragment light chain | protein | 214 | 3% helix, 52% strand | — |
| C | D80 Fab fragment heavy chain | protein | 209 | 4% helix, 50% strand | — |
| D | D80 Fab fragment heavy chain | protein | 214 | 4% helix, 49% strand | — |
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 620 | 0.67 | 0.77 | 80 | empty |
| 2 | 473 | 0.63 | 0.76 | 67 | empty |
| 3 | 217 | 0.49 | 0.75 | 29 | empty |
| 4 | 96 | 0.40 | 0.77 | 19 | empty |
| 5 | 126 | 0.38 | 0.73 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1649 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1621 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 719 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 5JQD · PDBe 5JQD
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