Research workbench
AMC009 SOSIP.V4.2 in complex with PGV04 Fab
Analyse AMC009 SOSIP.V4.2 in complex with PGV04 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VO3
- Type
- protein
- Length
- 2,334 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PGV04 heavy chain; PGV04 light chain; AMC009 SOSIP.V4.2 envelope glycoprotein GP120…
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 4 distinct chains · 21% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, G, I | PGV04 heavy chain | protein | 125 | 11% helix, 46% strand | — |
| L, J, K | PGV04 light chain | protein | 100 | 6% helix, 46% strand | — |
| A, C, D | AMC009 SOSIP.V4.2 envelope glycoprotein GP120 | protein | 429 | 15% helix, 40% strand | — |
| B, E, F | AMC009 SOSIP.V4.2 envelope glycoprotein GP41 | protein | 124 | 61% helix, 3% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 60 copies · chains A, H, L, B, C, G, J, E, D, I, K, F
- BMA · beta-D-mannopyranose · sugar · 12 copies
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains L, J, K
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 | 531 | 0.79 | 0.86 | 57 | empty |
| 2 | 736 | 0.78 | 0.83 | 81 | empty |
| 3 | 721 | 0.78 | 0.82 | 78 | empty |
| 4 | 362 | 0.71 | 0.84 | 52 | empty |
| 5 | 1048 | 0.69 | 0.74 | 102 | empty |
Interfaces
24 interfaces between chains.
- A–B · 2343 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 2340 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 2329 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1060 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 1058 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 glycan, 36 disulfide (N-glycosylation, disulfide).
Compared structures
- 6VO3 · AMC009 SOSIP.v4.2 in complex with PGV04 Fab · the same entry in another collection · chain G against G, 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 6VO3 · PDBe 6VO3
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