Research workbench
Vaccine-elicited nhp fp-targeting antibody DF2F-A.01 in complex with HIV fusion peptide (residue 512-519)
Analyse Vaccine-elicited nhp fp-targeting antibody DF2F-A.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
- 6PEF
- Type
- protein
- Length
- 875 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody DF2F-A.01 heavy chain; Antibody DF2F-A.01 light chain; HIV fusion peptide…
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Antibody DF2F-A.01 heavy chain | protein | 219 | 9% helix, 51% strand | — |
| B | Antibody DF2F-A.01 light chain | protein | 211 | 6% helix, 51% strand | — |
| C, F | HIV fusion peptide residue 512-519 | protein | 8 | 0% helix, 0% strand | — |
| E | Antibody DF2F-A.01 light chain | protein | 210 | 6% helix, 51% strand | — |
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.65 | 0.77 | 53 | empty |
| 2 | 163 | 0.46 | 0.76 | 28 | empty |
| 3 | 129 | 0.42 | 0.76 | 23 | empty |
| 4 | 110 | 0.36 | 0.74 | 16 | empty |
| 5 | 94 | 0.35 | 0.74 | 25 | empty |
Interfaces
9 interfaces between chains.
- D–E · 1720 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1707 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 402 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 401 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 383 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6PEF · Vaccine-elicited NHP FP-targeting antibody DF2F-a.01 in complex with HIV fusion peptide… · 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 6PEF · PDBe 6PEF
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