MolNFT v1 · #169287 · protein
Vaccine-elicited mouse fp-targeting neutralizing antibody VFP48.03 in complex with HIV fusion peptide (residue 512-519)
6X78 · Antibody VFP48.03 light chain: “Vaccine-elicited mouse fp-targeting neutralizing antibody VFP48.03 in complex with HIV fusion peptide…”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.63). MolNFT v1 #169287 on…
- PDB
- 6X78
- Type
- protein
- Length
- 887 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody VFP48.03 light chain; Antibody VFP48.03 heavy chain; HIV fusion peptide 512-519…
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | Antibody VFP48.03 light chain | protein | 218 | 6% helix, 51% strand | — |
| B | Antibody VFP48.03 heavy chain | protein | 218 | 7% helix, 51% strand | — |
| H | Antibody VFP48.03 heavy chain | protein | 223 | 7% helix, 49% strand | — |
| G, I | HIV fusion peptide 512-519 V2 | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 629 | 0.63 | 0.74 | 64 | empty |
| 2 | 527 | 0.61 | 0.74 | 53 | empty |
| 3 | 231 | 0.60 | 0.80 | 25 | SO4 |
| 4 | 211 | 0.53 | 0.78 | 32 | empty |
| 5 | 158 | 0.43 | 0.74 | 29 | empty |
Interfaces
9 interfaces between chains.
- H–L · 1889 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1811 Ų buried · 20 hydrogen bonds · protein-protein
- B–L · 246 Ų buried · 3 hydrogen bonds · protein-protein
- H–G · 194 Ų buried · 4 hydrogen bonds · protein-protein
- B–I · 186 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6X78 · Vaccine-elicited mouse FP-targeting neutralizing antibody vFP48.03 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 6X78 · PDBe 6X78
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