Research workbench
Vaccine-elicited NHP FP-targeting neutralizing antibody DF2F-b.04 in complex with HIV fusion peptide (residue 512-519)
Analyse Vaccine-elicited NHP FP-targeting neutralizing antibody DF2F-b.04 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P7H
- Type
- protein
- Length
- 437 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.782
- Source
- Platyrrhini; SYNTHETIC CONSTRUCT
- Molecule
- Antibody DF2F-b.04 light chain; Antibody DF2F-b.04 heavy chain; HIV fusion peptide…
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · resolution 1.782 · 3 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Antibody DF2F-b.04 light chain | protein | 214 | 6% helix, 50% strand | — |
| A | Antibody DF2F-b.04 heavy chain | protein | 215 | 6% helix, 52% strand | — |
| C | HIV fusion peptide residues (512-519) | protein | 8 | 38% 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 | 450 | 0.58 | 0.74 | 58 | empty |
| 2 | 61 | 0.27 | 0.73 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–A · 1695 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 367 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 338 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6P7H · Vaccine-elicited nhp fp-targeting neutralizing antibody DF2F-B.04 in complex with HIV… · 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 6P7H · PDBe 6P7H
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