Research workbench
Rhesusized RV144 DH827 Fab bound to HIV-1 env V2 peptide
Analyse Rhesusized RV144 DH827 Fab bound to HIV-1 env V2 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N0X
- Type
- protein
- Length
- 446 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhesusized RV144 DH827 heavy chain Fab fragment; Rhesusized RV144 DH827 light chain…
- UniProt
- Q70992
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Rhesusized RV144 DH827 heavy chain Fab fragment | protein | 217 | 6% helix, 51% strand | — |
| L | Rhesusized RV144 DH827 light chain | protein | 211 | 8% helix, 49% strand | — |
| G | Glycoprotein 120 | protein | 18 | 67% helix, 0% strand | Q70992 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 462 | 0.58 | 0.74 | 54 | empty |
| 2 | 148 | 0.45 | 0.76 | 40 | empty |
| 3 | 62 | 0.39 | 0.80 | 17 | empty |
| 4 | 99 | 0.38 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1681 Ų buried · 13 hydrogen bonds · protein-protein
- H–G · 546 Ų buried · 5 hydrogen bonds · protein-protein
- L–G · 340 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7N0X · Rhesusized RV144 DH827 Fab bound to HIV-1 Env 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 Q70992
- Elsewhere: RCSB PDB 7N0X · PDBe 7N0X · UniProt Q70992
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