Research workbench
Structure of mouse vaccination-elicited HIV neutralizing antibody VFP5.01 in complex with HIV-1 fusion peptide residue 512-519
Analyse Structure of mouse vaccination-elicited HIV neutralizing antibody VFP5.01 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TKK
- Type
- protein
- Length
- 434 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 fusion peptide residue 512-519; Mouse antibody VFP5.01 heavy chain; Mouse antibody…
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 fusion peptide residue 512-519 | protein | 8 | 38% helix, 0% strand | — |
| H | Mouse antibody VFP5.01 heavy chain | protein | 213 | 6% helix, 55% strand | — |
| L | Mouse antibody VFP5.01 light chain | protein | 213 | 7% helix, 50% strand | — |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 457 | 0.61 | 0.75 | 45 | empty |
| 2 | 77 | 0.34 | 0.75 | 16 | empty |
| 3 | 85 | 0.33 | 0.74 | 20 | empty |
| 4 | 70 | 0.32 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1851 Ų buried · 12 hydrogen bonds · protein-protein
- A–H · 362 Ų buried · 5 hydrogen bonds · protein-protein
- A–L · 265 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5TKK · Structure of mouse vaccination-elicited HIV neutralizing antibody vFP5.01 in complex with… · 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 5TKK · PDBe 5TKK
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