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Structure of vaccine-elicited diverse HIV-1 neutralizing antibody VFP1.01 in complex with HIV-1 fusion peptide residue 512-519
Analyse Structure of vaccine-elicited diverse HIV-1 neutralizing antibody VFP1.01 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TKJ
- Type
- protein
- Length
- 1,742 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VFP1.01 chimeric mouse antibody heavy chain; VFP1.01 chimeric mouse antibody light chain…
- Ligands
- SO4
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, J | VFP1.01 chimeric mouse antibody heavy chain | protein | 211 | 9% helix, 53% strand | — |
| B | VFP1.01 chimeric mouse antibody light chain | protein | 218 | 6% helix, 50% strand | — |
| C, F, I, L | HIV-1 fusion peptide residue 512-519 | protein | 8 | 0% helix, 0% strand | — |
| E | VFP1.01 chimeric mouse antibody light chain | protein | 219 | 5% helix, 50% strand | — |
| G | VFP1.01 chimeric mouse antibody heavy chain | protein | 208 | 9% helix, 50% strand | — |
| H, K | VFP1.01 chimeric mouse antibody light chain | protein | 216 | 6% helix, 52% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, D, J, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1144 | 0.84 | 0.85 | 107 | SO4 |
| 2 | 746 | 0.65 | 0.74 | 91 | empty |
| 3 | 729 | 0.64 | 0.74 | 81 | empty |
| 4 | 692 | 0.63 | 0.73 | 72 | empty |
| 5 | 707 | 0.63 | 0.73 | 85 | empty |
Interfaces
20 interfaces between chains.
- G–H · 1729 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1708 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 1702 Ų buried · 11 hydrogen bonds · protein-protein
- J–K · 1682 Ų buried · 7 hydrogen bonds · protein-protein
- D–G · 861 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 5TKJ · Structure of vaccine-elicited diverse HIV-1 neutralizing antibody vFP1.01 in complex with… · the same entry in another collection · chain H against H, 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 5TKJ · PDBe 5TKJ
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