MolNFT v1 · #116933 · protein
Crystal structure of human Fab CAP256-VRC26.25, a potent V1V2-directed HIV-1 broadly neutralizing antibody
5DT1 · Fab heavy chain of broadly neutralizing antibody VRC26.25: “Crystal structure of human Fab CAP256-VRC26.25, a potent V1V2-directed HIV-1 broadly neutralizing antibody”. X-ray diffraction, 2 ligands (NAG, BMA), 3 pockets (best…
- PDB
- 5DT1
- Type
- protein
- Length
- 460 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab heavy chain of broadly neutralizing antibody VRC26.25; Fab light chain of broadly…
- Ligands
- NAG, BMA
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab heavy chain of broadly neutralizing antibody VRC26.25 | protein | 245 | 8% helix, 53% strand | — |
| L | Fab light chain of broadly neutralizing antibody VRC26.25 | protein | 215 | 9% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains L
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 799 | 0.71 | 0.77 | 90 | empty |
| 2 | 131 | 0.47 | 0.78 | 24 | empty |
| 3 | 90 | 0.39 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- H–L · 1999 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 modified, 1 glycan (disulfide, sulfation, N-glycosylation).
Compared structures
- 5DT1 · Crystal structure of human Fab CAP256-VRC26.25, a potent V1V2-directed HIV-1 broadly… · 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 5DT1 · PDBe 5DT1
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