Research workbench
Crystal structure of the Fab fragment of a humanized HBV therapeutic antibody
Analyse Crystal structure of the Fab fragment of a humanized HBV therapeutic antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L8T
- Type
- protein
- Length
- 1,317 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody light chain; Antibody heavy chain
- Pockets
- 19 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, B, D | Antibody light chain | protein | 219 | 5% helix, 51% strand | — |
| H, A, C | Antibody heavy chain | protein | 220 | 5% helix, 50% strand | — |
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.73 | 0.83 | 53 | empty |
| 2 | 632 | 0.71 | 0.78 | 80 | empty |
| 3 | 668 | 0.66 | 0.75 | 53 | empty |
| 4 | 313 | 0.63 | 0.79 | 43 | empty |
| 5 | 421 | 0.59 | 0.75 | 52 | empty |
Interfaces
9 interfaces between chains.
- D–C · 2115 Ų buried · 16 hydrogen bonds · protein-protein
- B–A · 1967 Ų buried · 17 hydrogen bonds · protein-protein
- L–H · 1881 Ų buried · 12 hydrogen bonds · protein-protein
- H–D · 512 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 382 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 6L8T · Crystal structure of the Fab fragment of a humanized HBV therapeutic antibody · 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 6L8T · PDBe 6L8T
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