Research workbench
Crystal structure of RV144-elicited antibody CH58 in complex with V2 peptide
Analyse Crystal structure of RV144-elicited antibody CH58 in complex with V2 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HPO
- Type
- protein
- Length
- 445 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CH58 Fab heavy chain; CH58 Fab light chain; Envelope glycoprotein GP160
- UniProt
- Q9WLG7
- Ligands
- NAG, FUC
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | CH58 Fab heavy chain | protein | 217 | 8% helix, 53% strand | — |
| L | CH58 Fab light chain | protein | 213 | 9% helix, 51% strand | — |
| P | Envelope glycoprotein GP160 | protein | 15 | 60% helix, 0% strand | Q9WLG7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains L
- FUC · alpha-L-fucopyranose · sugar · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.52 | 0.75 | 35 | empty |
| 2 | 90 | 0.31 | 0.73 | 21 | empty |
| 3 | 56 | 0.24 | 0.72 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1642 Ų buried · 13 hydrogen bonds · protein-protein
- H–P · 632 Ų buried · 12 hydrogen bonds · protein-protein
- L–P · 379 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4HPO · Crystal structure of RV144-elicited antibody CH58 in complex with V2 peptide · the same entry in another collection · chain H against H, 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 Q9WLG7
- Elsewhere: RCSB PDB 4HPO · PDBe 4HPO · UniProt Q9WLG7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.