Research workbench
Fab fragment of a neutralizing antibody directed against an epitope of GP41 from HIV-1
Analyse Fab fragment of a neutralizing antibody directed against an epitope of GP41… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NLD
- Type
- protein
- Length
- 434 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAB1583
- Pockets
- 6 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | FAB1583 | protein | 219 | 5% helix, 49% strand | — |
| H | FAB1583 | protein | 215 | 5% helix, 48% strand | — |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.51 | 0.73 | 46 | empty |
| 2 | 118 | 0.47 | 0.79 | 18 | empty |
| 3 | 101 | 0.42 | 0.78 | 20 | empty |
| 4 | 84 | 0.34 | 0.74 | 20 | empty |
| 5 | 78 | 0.30 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- L–H · 1788 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1NLD · Fab fragment of a neutralizing antibody directed against an epitope of GP41 from HIV-1 · 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 1NLD · PDBe 1NLD
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