Research workbench
N123-VRC34_PI4 HIV neutralizing antibody in complex with HIV fusion peptide residue 512-519
Analyse N123-VRC34_PI4 HIV neutralizing antibody in complex with HIV fusion peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UCF
- Type
- protein
- Length
- 447 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N123-VRC34_PI4 light chain; N123-VRC34_PI4 heavy chain; HIV fusion peptide
- UniProt
- Q6GMX0
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | N123-VRC34_PI4 light chain | protein | 213 | 6% helix, 51% strand | Q6GMX0 |
| H | N123-VRC34_PI4 heavy chain | protein | 226 | 12% helix, 49% strand | — |
| A | HIV fusion peptide | protein | 8 | 0% helix, 0% strand | — |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.59 | 0.75 | 54 | empty |
| 2 | 200 | 0.49 | 0.76 | 31 | empty |
| 3 | 62 | 0.48 | 0.85 | 21 | empty |
| 4 | 94 | 0.35 | 0.74 | 26 | empty |
| 5 | 53 | 0.27 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1882 Ų buried · 13 hydrogen bonds · protein-protein
- H–A · 459 Ų buried · 8 hydrogen bonds · protein-protein
- L–A · 182 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6UCF · N123-VRC34_pI4 HIV neutralizing antibody in complex with HIV fusion peptide residue… · the same entry in another collection · chain L against L, 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
- Every structure of UniProt Q6GMX0
- Elsewhere: RCSB PDB 6UCF · PDBe 6UCF · UniProt Q6GMX0
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