Research workbench
Vaccine-elicited nhp fp-targeting antibody DF2F-E.01 in complex with HIV fusion peptide (residue 512-519)
Analyse Vaccine-elicited nhp fp-targeting antibody DF2F-E.01 in complex with HIV fusion… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PEC
- Type
- protein
- Length
- 432 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody light chain; Antibody heavy chain; HIV-1 fusion peptide residue 512-519
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Antibody light chain | protein | 208 | 5% helix, 50% strand | — |
| H | Antibody heavy chain | protein | 216 | 7% helix, 54% strand | — |
| A | HIV-1 fusion peptide residue 512-519 | protein | 8 | 50% helix, 0% strand | — |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.55 | 0.74 | 46 | empty |
| 2 | 58 | 0.27 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1723 Ų buried · 17 hydrogen bonds · protein-protein
- H–A · 368 Ų buried · 4 hydrogen bonds · protein-protein
- L–A · 275 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6PEC · Vaccine-elicited NHP FP-targeting antibody DF2F-e.01 in complex with HIV fusion peptide… · 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 6PEC · PDBe 6PEC
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