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
- 6EMJ
- Type
- protein
- Length
- 854 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab heavy chain; Fab light chain
- Ligands
- NA
- Pockets
- 13 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab heavy chain | protein | 212 | 8% helix, 54% strand | — |
| B | Fab light chain | protein | 213 | 5% helix, 51% strand | — |
| H | Fab heavy chain | protein | 218 | 8% helix, 53% strand | — |
| L | Fab light chain | protein | 211 | 6% helix, 52% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 541 | 0.70 | 0.80 | 75 | empty |
| 2 | 397 | 0.63 | 0.78 | 36 | empty |
| 3 | 145 | 0.54 | 0.81 | 25 | empty |
| 4 | 151 | 0.51 | 0.80 | 42 | empty |
| 5 | 130 | 0.51 | 0.80 | 23 | empty |
Interfaces
5 interfaces between chains.
- H–L · 1922 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1807 Ų buried · 17 hydrogen bonds · protein-protein
- B–L · 719 Ų buried · 13 hydrogen bonds · protein-protein
- A–L · 57 Ų buried · 1 hydrogen bond · protein-protein
- B–H · 22 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6EMJ · 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 6EMJ · PDBe 6EMJ
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