Research workbench
Structural analysis of the unmutated ancestor of the HIV-1 envelope V2 region antibody CH58 isolated from an RV144 HIV-1 vaccine efficacy trial vaccinee and associated with decreased transmission risk
Analyse Structural analysis of the unmutated ancestor of the HIV-1 envelope V2 region… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RIR
- Type
- protein
- Length
- 866 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CH58-ua Fab heavy chain; CH58-ua Fab light chain
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, A | CH58-ua Fab heavy chain | protein | 219 | 9% helix, 49% strand | — |
| L, B | CH58-ua Fab light chain | protein | 214 | 9% helix, 50% strand | — |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.71 | 0.75 | 100 | empty |
| 2 | 693 | 0.65 | 0.75 | 82 | empty |
| 3 | 52 | 0.32 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1746 Ų buried · 18 hydrogen bonds · protein-protein
- H–L · 1719 Ų buried · 21 hydrogen bonds · protein-protein
- L–A · 187 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4RIR · Structural Analysis of the Unmutated Ancestor of the HIV-1 Envelope V2 Region Antibody… · 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
- Elsewhere: RCSB PDB 4RIR · PDBe 4RIR
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