Research workbench
Fab fragment. abvance: increasing our knowledge of antibody structural space to enable faster and better decision making in antibody drug discovery
Analyse Fab fragment. abvance: increasing our knowledge of antibody structural space to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ELJ
- Type
- protein
- Length
- 867 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab heavy chain; Fab light chain
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab heavy chain | protein | 224 | 9% helix, 52% strand | — |
| B | Fab light chain | protein | 213 | 5% helix, 52% strand | — |
| H | Fab heavy chain | protein | 218 | 8% helix, 52% strand | — |
| L | Fab light chain | protein | 212 | 5% helix, 52% strand | — |
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 761 | 0.75 | 0.80 | 83 | empty |
| 2 | 342 | 0.67 | 0.82 | 28 | empty |
| 3 | 165 | 0.58 | 0.82 | 33 | empty |
| 4 | 122 | 0.55 | 0.82 | 18 | empty |
| 5 | 169 | 0.54 | 0.80 | 28 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2108 Ų buried · 21 hydrogen bonds · protein-protein
- H–L · 1872 Ų buried · 17 hydrogen bonds · protein-protein
- B–L · 884 Ų buried · 15 hydrogen bonds · protein-protein
- A–L · 128 Ų buried · 1 hydrogen bond · protein-protein
- B–H · 43 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6ELJ · FAB Fragment. AbVance: Increasing our knowledge of antibody structural space to enable… · the same entry in another collection · chain A against A, 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 6ELJ · PDBe 6ELJ
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