Research workbench
Vaccine-elicited mouse fp-targeting neutralizing antibody VFP16.02 with F60P mutation on light chain in complex with HIV fusion peptide (residue 512-519)
Analyse Vaccine-elicited mouse fp-targeting neutralizing antibody VFP16.02 with F60P… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WX2
- Type
- protein
- Length
- 872 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VFP16.02 antibody heavy chain; VFP16.02 antibody light chain; Fusion peptide
- Pockets
- 11 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | VFP16.02 antibody heavy chain | protein | 210 | 7% helix, 54% strand | — |
| B, L | VFP16.02 antibody light chain | protein | 218 | 6% helix, 51% strand | — |
| C, F | Fusion peptide | protein | 8 | 0% helix, 0% strand | — |
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.66 | 0.81 | 49 | empty |
| 2 | 472 | 0.61 | 0.76 | 50 | empty |
| 3 | 246 | 0.60 | 0.80 | 47 | empty |
| 4 | 256 | 0.60 | 0.80 | 46 | empty |
| 5 | 164 | 0.51 | 0.79 | 24 | empty |
Interfaces
9 interfaces between chains.
- H–L · 1856 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1842 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 1009 Ų buried · 8 hydrogen bonds · protein-protein
- H–F · 371 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 365 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6WX2 · Vaccine-elicited mouse FP-targeting neutralizing antibody vFP16.02 with F60P mutation on… · 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 6WX2 · PDBe 6WX2
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