Research workbench
Vaccine-elicited murine fp-targeting antibody VFP25.18 in complex with HIV fusion peptide (residue 512-519)
Analyse Vaccine-elicited murine fp-targeting antibody VFP25.18 in complex with HIV… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PDR
- Type
- protein
- Length
- 439 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody VFP25.18 light chain; Antibody VFP25.18 heavy chain; HIV fusion peptide residue…
- Pockets
- 4 · best druggability 0.42
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Antibody VFP25.18 light chain | protein | 218 | 7% helix, 51% strand | — |
| H | Antibody VFP25.18 heavy chain | protein | 213 | 6% helix, 55% strand | — |
| A | HIV fusion peptide residue 512-519 | protein | 8 | 0% helix, 13% strand | — |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.42 | 0.73 | 32 | empty |
| 2 | 128 | 0.41 | 0.75 | 24 | empty |
| 3 | 105 | 0.40 | 0.76 | 24 | empty |
| 4 | 54 | 0.25 | 0.73 | 16 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1526 Ų buried · 13 hydrogen bonds · protein-protein
- L–A · 370 Ų buried · 0 hydrogen bonds · protein-protein
- H–A · 355 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6PDR · Vaccine-elicited murine FP-targeting antibody vFP25.18 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 6PDR · PDBe 6PDR
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