MolNFT v1 · #160023 · protein
Vaccine-elicited murine fp-targeting antibody VFP6.01 in complex with HIV fusion peptide (residue 512-519)
6P8D · Antibody VFP6.01 heavy chain: “Vaccine-elicited murine fp-targeting antibody VFP6.01 in complex with HIV fusion peptide (residue 512-519)”. X-ray diffraction, 6 pockets (best druggability 0.69). MolNFT v1 #160023 on GenesisL1: 3D…
- PDB
- 6P8D
- Type
- protein
- Length
- 869 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody VFP6.01 heavy chain; Antibody VFP6.01 light chain; HIV fusion peptide residue…
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody VFP6.01 heavy chain | protein | 211 | 4% helix, 51% strand | — |
| B, E | Antibody VFP6.01 light chain | protein | 216 | 6% helix, 49% strand | — |
| D | Antibody VFP6.01 heavy chain | protein | 210 | 4% helix, 52% strand | — |
| F, C | HIV fusion peptide residue 512-519 | protein | 8 | 0% helix, 13% strand | — |
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.69 | 0.76 | 61 | empty |
| 2 | 416 | 0.66 | 0.79 | 51 | empty |
| 3 | 677 | 0.64 | 0.74 | 65 | empty |
| 4 | 485 | 0.61 | 0.75 | 49 | empty |
| 5 | 249 | 0.56 | 0.78 | 29 | empty |
Interfaces
9 interfaces between chains.
- D–E · 1790 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1664 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 436 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 418 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 396 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6P8D · Vaccine-elicited murine FP-targeting antibody vFP6.01 in complex with HIV fusion peptide… · 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 6P8D · PDBe 6P8D
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