Research workbench
X-ray structure of the Fab fragment of 15B8, a murine monoclonal antibody specific for the human serotonin transporter
Analyse X-ray structure of the Fab fragment of 15B8, a murine monoclonal antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D9G
- Type
- protein
- Length
- 875 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody heavy chain Fab; Antibody light chain Fab
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody heavy chain Fab | protein | 222 | 9% helix, 51% strand | — |
| B, D | Antibody light chain Fab | protein | 216 | 6% helix, 53% strand | — |
| C | Antibody heavy chain Fab | protein | 221 | 7% helix, 51% strand | — |
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 815 | 0.68 | 0.75 | 96 | empty |
| 2 | 472 | 0.60 | 0.75 | 51 | empty |
| 3 | 488 | 0.59 | 0.74 | 45 | empty |
| 4 | 376 | 0.55 | 0.74 | 51 | empty |
| 5 | 181 | 0.43 | 0.74 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1934 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1916 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 405 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 361 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 15 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6D9G · X-ray Structure of the FAB Fragment of 15B8, a Murine Monoclonal Antibody Specific for… · 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 6D9G · PDBe 6D9G
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