MolNFT v1 · #186858 · protein
AMC016 SOSIP.V4.2 in complex with PGV04 Fab
7RSO · AMC016 GP120: “AMC016 SOSIP.V4.2 in complex with PGV04 Fab”. Electron microscopy, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.78). MolNFT v1 #186858 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7RSO
- Type
- protein
- Length
- 2,355 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AMC016 GP120; AMC016 GP41; PGV04 Fab heavy chain; PGV04 kappa chain
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 4 distinct chains · 21% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | AMC016 GP120 | protein | 437 | 14% helix, 42% strand | — |
| B, E, F | AMC016 GP41 | protein | 124 | 63% helix, 6% strand | — |
| H, G, I | PGV04 Fab heavy chain | protein | 124 | 13% helix, 44% strand | — |
| L, J, K | PGV04 kappa chain | protein | 100 | 6% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 117 copies · chains A, H, L, C, G, J, D, I, K, B, E, F
- MAN · alpha-D-mannopyranose · sugar · 15 copies · chains A, L, C, J, D, K
- BMA · beta-D-mannopyranose · sugar · 12 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 | 660 | 0.78 | 0.83 | 87 | empty |
| 2 | 126 | 0.73 | 0.93 | 22 | empty |
| 3 | 1086 | 0.73 | 0.76 | 104 | empty |
| 4 | 678 | 0.71 | 0.78 | 71 | empty |
| 5 | 127 | 0.71 | 0.91 | 19 | empty |
Interfaces
27 interfaces between chains.
- A–B · 2418 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 2414 Ų buried · 17 hydrogen bonds · protein-protein
- C–E · 2411 Ų buried · 17 hydrogen bonds · protein-protein
- A–H · 1012 Ų buried · 16 hydrogen bonds · protein-protein
- D–I · 1009 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 81 glycan, 33 disulfide (N-glycosylation, disulfide).
Compared structures
- 7RSO · AMC016 SOSIP.v4.2 in complex with PGV04 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 7RSO · PDBe 7RSO
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