Research workbench
Vaccine-elicited nhp fp-targeting neutralizing antibody 0PV-B.01 in complex with HIV fusion peptide (residue 512-519)
Analyse Vaccine-elicited nhp fp-targeting neutralizing antibody 0PV-B.01 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N16
- Type
- protein
- Length
- 1,774 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody 0PV-B.01 Fab heavy chain; Antibody 0PV-B.01 Fab light chain; HIV fusion peptide…
- Pockets
- 18 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody 0PV-B.01 Fab heavy chain | protein | 217 | 8% helix, 53% strand | — |
| B, J, L, D | Antibody 0PV-B.01 Fab light chain | protein | 217 | 6% helix, 51% strand | — |
| H, K, C | Antibody 0PV-B.01 Fab heavy chain | protein | 219 | 6% helix, 50% strand | — |
| E, F, G, I | HIV fusion peptide (512-519) | protein | 8 | 0% helix, 0% strand | — |
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.71 | 0.79 | 72 | empty |
| 2 | 776 | 0.68 | 0.75 | 90 | empty |
| 3 | 648 | 0.67 | 0.76 | 71 | empty |
| 4 | 333 | 0.61 | 0.78 | 44 | empty |
| 5 | 416 | 0.60 | 0.76 | 56 | empty |
Interfaces
18 interfaces between chains.
- H–L · 1785 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1764 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1729 Ų buried · 13 hydrogen bonds · protein-protein
- J–K · 1695 Ų buried · 14 hydrogen bonds · protein-protein
- B–L · 901 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 6N16 · Vaccine-elicited NHP FP-targeting neutralizing antibody 0PV-b.01 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 6N16 · PDBe 6N16
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