Research workbench
Structure of full-length, fully glycosylated, non-modified HIV-1 GP160 bound to PG16 Fab
Analyse Structure of full-length, fully glycosylated, non-modified HIV-1 GP160 bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PWU
- Type
- protein
- Length
- 2,301 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; Antibody PG16 Fab heavy chain; Antibody PG16 Fab light chain
- UniProt
- Q71014
- Ligands
- NAG, BMA, MAN, FUC, GAL
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 14% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Envelope glycoprotein GP160 | protein | 615 | 21% helix, 23% strand | Q71014 |
| H | Antibody PG16 Fab heavy chain | protein | 240 | 4% helix, 49% strand | — |
| L | Antibody PG16 Fab light chain | protein | 216 | 9% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 109 copies · chains A, C, H, E, L
- BMA · beta-D-mannopyranose · sugar · 21 copies · chains H, L, A, E
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains H, L
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains C, A
- GAL · beta-D-galactopyranose · sugar · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.86 | 0.87 | 135 | empty |
| 2 | 1109 | 0.83 | 0.84 | 131 | empty |
| 3 | 173 | 0.82 | 0.96 | 33 | empty |
| 4 | 195 | 0.82 | 0.95 | 36 | empty |
| 5 | 121 | 0.80 | 0.97 | 24 | empty |
Interfaces
6 interfaces between chains.
- H–L · 2047 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1796 Ų buried · 15 hydrogen bonds · protein-protein
- C–E · 1666 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 1660 Ų buried · 22 hydrogen bonds · protein-protein
- A–H · 494 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 79 glycan, 46 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 6PWU · Structure of full-length, fully glycosylated, non-modified HIV-1 gp160 bound to PG16 Fab · 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
- Every structure of UniProt Q71014
- Elsewhere: RCSB PDB 6PWU · PDBe 6PWU · UniProt Q71014
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