Research workbench
FAB/EPITOPE complex structure of rabbit monoclonal antibody R53 targeting an epitope in HIV-1 GP120 C4 region
Analyse FAB/EPITOPE complex structure of rabbit monoclonal antibody R53 targeting an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZTO
- Type
- protein
- Length
- 895 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rabbit monoclonal antibody R53 Fab light chain; Rabbit monoclonal antibody R53 Fab heavy…
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M | Rabbit monoclonal antibody R53 Fab light chain | protein | 216 | 5% helix, 55% strand | — |
| H, I | Rabbit monoclonal antibody R53 Fab heavy chain | protein | 221 | 3% helix, 51% strand | — |
| P | Epitope of rabbit monoclonal antibody R53 | protein | 11 | 0% helix, 0% strand | — |
| Q | Epitope of rabbit monoclonal antibody R53 | protein | 10 | 0% helix, 0% 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 | 397 | 0.67 | 0.80 | 49 | empty |
| 2 | 514 | 0.61 | 0.74 | 54 | empty |
| 3 | 477 | 0.61 | 0.75 | 49 | empty |
| 4 | 68 | 0.54 | 0.86 | 19 | empty |
| 5 | 203 | 0.50 | 0.76 | 23 | empty |
Interfaces
9 interfaces between chains.
- M–I · 2017 Ų buried · 22 hydrogen bonds · protein-protein
- L–H · 2011 Ų buried · 21 hydrogen bonds · protein-protein
- I–Q · 400 Ų buried · 3 hydrogen bonds · protein-protein
- L–P · 397 Ų buried · 8 hydrogen bonds · protein-protein
- H–I · 377 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 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 4ZTO · PDBe 4ZTO
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