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Structure of vaccine-elicited HIV-1 neutralizing antibody VFP7.04 in complex with HIV-1 fusion peptide residue 512-519
Analyse Structure of vaccine-elicited HIV-1 neutralizing antibody VFP7.04 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CDM
- Type
- protein
- Length
- 884 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VFP7.04 heavy chain; VFP7.04 light chain; HIV fusion peptide (512-519)
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | VFP7.04 heavy chain | protein | 218 | 8% helix, 53% strand | — |
| B, E | VFP7.04 light chain | protein | 218 | 5% helix, 51% strand | — |
| C, F | HIV fusion peptide (512-519) | protein | 6 | 0% helix, 0% strand | — |
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1032 | 0.71 | 0.75 | 101 | empty |
| 2 | 613 | 0.63 | 0.74 | 62 | empty |
| 3 | 52 | 0.51 | 0.88 | 22 | empty |
| 4 | 200 | 0.45 | 0.74 | 34 | empty |
| 5 | 83 | 0.36 | 0.76 | 21 | empty |
Interfaces
7 interfaces between chains.
- D–E · 1881 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1871 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 497 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 329 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 319 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6CDM · Structure of vaccine-elicited HIV-1 neutralizing antibody vFP7.04 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 6CDM · PDBe 6CDM
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