MolNFT v1 · #145086 · protein
Structure of vaccine-elicited HIV-1 neutralizing antibody VFP16.02 in complex with HIV-1 fusion peptide residue 512-519
6CDO · VFP16.02 Fab heavy chain: “Structure of vaccine-elicited HIV-1 neutralizing antibody VFP16.02 in complex with HIV-1 fusion peptide…”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.63). MolNFT v1 #145086 on…
- PDB
- 6CDO
- Type
- protein
- Length
- 457 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VFP16.02 Fab heavy chain; VFP16.02 Fab light chain; HIV-1 fusion peptide 512-519
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VFP16.02 Fab heavy chain | protein | 230 | 9% helix, 49% strand | — |
| B | VFP16.02 Fab light chain | protein | 219 | 6% helix, 52% strand | — |
| C | HIV-1 fusion peptide 512-519 | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 634 | 0.63 | 0.74 | 64 | empty |
| 2 | 52 | 0.62 | 0.94 | 16 | empty |
| 3 | 92 | 0.48 | 0.81 | 25 | empty |
| 4 | 129 | 0.44 | 0.76 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2316 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 359 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 241 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6CDO · Structure of vaccine-elicited HIV-1 neutralizing antibody vFP16.02 in complex with HIV-1… · 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 6CDO · PDBe 6CDO
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