Research workbench
Full length HIV-1 env AMC011 in complex with PGT151 Fab
Analyse Full length HIV-1 env AMC011 in complex with PGT151 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OLP
- Type
- protein
- Length
- 2,182 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120; Envelope glycoprotein GP41; Immunoglobulin G PGT151 Fab…
- Ligands
- NAG, MAN, BMA, FUC, GAL
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 10 distinct chains · 16% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein GP120 | protein | 430 | 10% helix, 32% strand | — |
| B | Envelope glycoprotein GP41 | protein | 143 | 55% helix, 5% strand | — |
| C | Envelope glycoprotein GP120 | protein | 438 | 11% helix, 26% strand | — |
| D | Envelope glycoprotein GP41 | protein | 129 | 50% helix, 9% strand | — |
| E | Envelope glycoprotein GP120 | protein | 419 | 11% helix, 36% strand | — |
| F | Envelope glycoprotein GP41 | protein | 134 | 47% helix, 3% strand | — |
| G | Immunoglobulin G PGT151 Fab, heavy chain | protein | 134 | 4% helix, 40% strand | — |
| I | Immunoglobulin G PGT151 Fab, light chain | protein | 109 | 0% helix, 41% strand | — |
| H | Immunoglobulin G PGT151 Fab, heavy chain | protein | 135 | 0% helix, 41% strand | — |
| L | Immunoglobulin G PGT151 Fab, light chain | protein | 111 | 0% helix, 33% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 96 copies · chains A, B, G, I, C, D, E, H, L, F
- MAN · alpha-D-mannopyranose · sugar · 11 copies · chains G, I, C, H, L
- BMA · beta-D-mannopyranose · sugar · 8 copies · chains G, H
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains G, I, B, C, D, H
- GAL · beta-D-galactopyranose · sugar · 5 copies · chains I, G, H, L, F
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 | 985 | 0.84 | 0.85 | 102 | empty |
| 2 | 466 | 0.78 | 0.86 | 72 | NAG |
| 3 | 606 | 0.78 | 0.83 | 57 | empty |
| 4 | 492 | 0.77 | 0.84 | 57 | empty |
| 5 | 73 | 0.75 | 0.97 | 15 | empty |
Interfaces
25 interfaces between chains.
- A–B · 2953 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 2404 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 2352 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 1186 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1136 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 66 glycan, 34 disulfide (N-glycosylation, disulfide).
Compared structures
- 6OLP · Full length HIV-1 Env AMC011 in complex with PGT151 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
- Elsewhere: RCSB PDB 6OLP · PDBe 6OLP
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