MolNFT v1 · #168959 · protein
Vaccine-elicited mouse fp-targeting neutralizing antibody VFP16.02 with S48K mutation in light chain in complex with HIV fusion peptide (residue 512-519)
6WWC · VFP16.02 antibody heavy chain: “Vaccine-elicited mouse fp-targeting neutralizing antibody VFP16.02 with S48K mutation in light chain in…”. X-ray diffraction, 9 pockets (best druggability 0.68). MolNFT v1 #168959 on GenesisL1: 3D…
- PDB
- 6WWC
- Type
- protein
- Length
- 878 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VFP16.02 antibody heavy chain; VFP16.02 antibody light chain; Fusion peptide
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | VFP16.02 antibody heavy chain | protein | 213 | 6% helix, 52% strand | — |
| B, H | VFP16.02 antibody light chain | protein | 218 | 5% helix, 55% strand | — |
| C, F | Fusion peptide | protein | 8 | 0% helix, 0% strand | — |
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 720 | 0.68 | 0.76 | 56 | empty |
| 2 | 780 | 0.68 | 0.75 | 58 | empty |
| 3 | 406 | 0.64 | 0.78 | 58 | empty |
| 4 | 63 | 0.51 | 0.86 | 19 | empty |
| 5 | 190 | 0.43 | 0.73 | 31 | empty |
Interfaces
8 interfaces between chains.
- D–H · 1879 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1839 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 772 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 342 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 342 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6WWC · Vaccine-elicited mouse FP-targeting neutralizing antibody vFP16.02 with S48K mutation in… · 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 6WWC · PDBe 6WWC
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