Structure of vaccine-elicited HIV-1 neutralizing antibody vFP16.02 in complex with HIV-1 fusion peptide residue 512-519. Determined by X-ray diffraction at 2.1 Å resolution. Released 16 May 2018.
Explore 6CDO in 3D Show helices and sheets RCSB PDB PDBe
6CDO contains 19 α-helices and 46 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 3-5 | 3 | 1 |
| β-strand | 9-12 | 4 | 2 |
| β-strand | 18-25 | 8 | 1 |
| α-helix | 29-31 | 3 | |
| β-strand | 33-40 | 8 | 2 |
| β-strand | 44-51 | 8 | 2 |
| β-strand | 58-60 | 3 | 2 |
| β-strand | 68-73 | 6 | 1 |
| β-strand | 78-83 | 6 | 1 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-99 | 8 | 2 |
| β-strand | 108 | 1 | 2 |
| β-strand | 112-116 | 5 | 2 |
| α-helix | 120-121 | 2 | |
| β-strand | 122 | 1 | 3 |
| α-helix | 123-124 | 2 | |
| β-strand | 125-129 | 5 | 4 |
| α-helix | 133-135 | 3 | |
| β-strand | 136-137 | 2 | 4 |
| β-strand | 140-150 | 11 | 4 |
| β-strand | 151 | 1 | 3 |
| β-strand | 156-159 | 4 | 5 |
| α-helix | 160-162 | 3 | |
| β-strand | 164 | 1 | 5 |
| β-strand | 168-170 | 3 | 4 |
| α-helix | 171-173 | 3 | |
| β-strand | 174-175 | 2 | 4 |
| β-strand | 181-190 | 10 | 4 |
| α-helix | 191-193 | 3 | |
| β-strand | 200-205 | 6 | 5 |
| α-helix | 206-208 | 3 | |
| β-strand | 210-215 | 6 | 5 |
| α-helix | 223-225 | 3 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 4-7 | 4 | 6 |
| β-strand | 10-14 | 5 | 7 |
| β-strand | 18-25 | 8 | 6 |
| β-strand | 30 | 1 | 8 |
| β-strand | 36 | 1 | 8 |
| β-strand | 38-43 | 6 | 7 |
| β-strand | 50-54 | 5 | 7 |
| β-strand | 58-59 | 2 | 7 |
| α-helix | 60 | 1 | |
| β-strand | 67-72 | 6 | 6 |
| β-strand | 75-81 | 7 | 6 |
| α-helix | 85-87 | 3 | |
| β-strand | 89-95 | 7 | 7 |
| α-helix | 101 | 1 | |
| β-strand | 102-103 | 2 | 7 |
| β-strand | 107-112 | 6 | 7 |
| β-strand | 116 | 1 | 9 |
| α-helix | 117-118 | 2 | |
| β-strand | 119-123 | 5 | 10 |
| α-helix | 124-126 | 3 | |
| α-helix | 127-132 | 6 | |
| β-strand | 134-144 | 11 | 10 |
| β-strand | 145 | 1 | 9 |
| β-strand | 150-155 | 6 | 11 |
| β-strand | 158-159 | 2 | 11 |
| α-helix | 160 | 1 | |
| β-strand | 164-168 | 5 | 10 |
| α-helix | 169-172 | 4 | |
| β-strand | 178-187 | 10 | 10 |
| α-helix | 188-192 | 5 | |
| β-strand | 196-202 | 7 | 11 |
| β-strand | 210-215 | 6 | 11 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| vFP16.02 Fab heavy chain | A | protein | 230 | Mus musculus | |
| vFP16.02 Fab light chain | B | protein | 219 | Mus musculus | |
| HIV-1 fusion peptide 512-519 | C | protein | 8 | Human immunodeficiency virus 1 | Q2N0S5 |
>6CDO_1 vFP16.02 Fab heavy chain (chains A) QVQLLQSGAELVRPGASVTLSCKASGYAFSDYEIHWVKQTPVRGLDWIGAFDPKSGASAS NQKVKGRAILTADKSSSTAYMELRSLTSEDSAVYYCTRLRYFGYFDVWGTGTTVTVSSAS TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ
>6CDO_2 vFP16.02 Fab light chain (chains B) DVLMTQTPLSLPVSLGGQASISCRSSQSVVYSDGDTYLEWYLQKPGQSPKLLIYKVSRRF SGVPDRFSGSGSGTDFTLKISRVETEDLGVYYCFQGSHVPYTFGGGTKLEIKRTVAAPSV FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
>6CDO_3 HIV-1 fusion peptide 512-519 (chains C) AVGIGAVF
Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1. Xu, K., Acharya, P., Kong, R. et al. Nat Med (2018) 24:857-867. DOI 10.1038/s41591-018-0042-6 · PubMed
Other PDB entries of the same protein (UniProt Q2N0S5), best resolution first:
MolViewer shows 6CDO directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.