Research workbench
Crystal structure of C11 Fab, an adcc mediating anti-HIV-1 antibody.
Analyse Crystal structure of C11 Fab, an adcc mediating anti-HIV-1 antibody. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FZ8
- Type
- protein
- Length
- 437 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab heavy chain of human anti-HIV-1 env antibody C11; Fab light chain of human anti-HIV-1…
- Ligands
- NAG, ZN
- Pockets
- 5 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab heavy chain of human anti-HIV-1 env antibody C11 | protein | 222 | 5% helix, 40% strand | — |
| L | Fab light chain of human anti-HIV-1 env antibody C11 | protein | 215 | 3% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
- ZN · Zinc ion · metal · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.48 | 0.74 | 35 | empty |
| 2 | 141 | 0.40 | 0.73 | 24 | empty |
| 3 | 135 | 0.39 | 0.74 | 21 | empty |
| 4 | 60 | 0.32 | 0.76 | 13 | empty |
| 5 | 85 | 0.31 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- H–L · 1869 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4FZ8 · Crystal structure of C11 Fab, an ADCC mediating anti-HIV-1 antibody. · the same entry in another collection · chain H against H, 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 4FZ8 · PDBe 4FZ8
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