Research workbench
Vaccine-elicited nhp fp-targeting antibody 13N024-A.01 in complex with HIV fusion peptide (residue 512-519)
Analyse Vaccine-elicited nhp fp-targeting antibody 13N024-A.01 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
- 6PDU
- Type
- protein
- Length
- 443 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody 13N024-A.01, light chain; Antibody 13N024-A.01, heavy chain; HIV-1 fusion…
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Antibody 13N024-A.01, light chain | protein | 219 | 6% helix, 51% strand | — |
| H | Antibody 13N024-A.01, heavy chain | protein | 216 | 10% helix, 51% strand | — |
| C | HIV-1 fusion peptide residue 512-519 | protein | 8 | 0% helix, 0% strand | — |
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 577 | 0.62 | 0.74 | 67 | empty |
| 2 | 129 | 0.51 | 0.80 | 29 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1783 Ų buried · 14 hydrogen bonds · protein-protein
- H–C · 352 Ų buried · 6 hydrogen bonds · protein-protein
- L–C · 347 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6PDU · Vaccine-elicited NHP FP-targeting antibody 13N024-a.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 6PDU · PDBe 6PDU
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