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Crystal structure of the disulfide linked DH717.1 Fab dimer, derived from a macaque HIV-1 vaccine-induced env glycan-reactive neutralizing antibody B cell lineage
Analyse Crystal structure of the disulfide linked DH717.1 Fab dimer, derived from a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XRJ
- Type
- protein
- Length
- 1,740 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DH717.1 heavy chain Fab fragment; DH717.1 light chain Fab fragment
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DH717.1 heavy chain Fab fragment | protein | 219 | 7% helix, 50% strand | — |
| B, D, F, L | DH717.1 light chain Fab fragment | protein | 211 | 8% helix, 53% strand | — |
| C, H | DH717.1 heavy chain Fab fragment | protein | 226 | 4% helix, 51% strand | — |
| E | DH717.1 heavy chain Fab fragment | protein | 225 | 3% helix, 51% strand | — |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.74 | 0.78 | 122 | empty |
| 2 | 572 | 0.66 | 0.77 | 57 | empty |
| 3 | 510 | 0.65 | 0.77 | 55 | empty |
| 4 | 377 | 0.64 | 0.79 | 48 | empty |
| 5 | 380 | 0.63 | 0.78 | 54 | empty |
Interfaces
11 interfaces between chains.
- H–L · 2002 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1926 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1915 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1854 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 809 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 6XRJ · Crystal structure of the disulfide linked DH717.1 Fab dimer, derived from a macaque HIV-1… · the same entry in another collection · chain A against A, 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 6XRJ · PDBe 6XRJ
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