MolNFT v1 · #186857 · protein
AMC018 SOSIP.V4.2 in complex with PGV04 Fab
7RSN · AMC018 GP120: “AMC018 SOSIP.V4.2 in complex with PGV04 Fab”. Electron microscopy, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.80). MolNFT v1 #186857 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7RSN
- Type
- protein
- Length
- 2,310 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AMC018 GP120; AMC018 GP41; PGV04 Fab heavy chain; PGV04 kappa chain
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 4 distinct chains · 17% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | AMC018 GP120 | protein | 421 | 13% helix, 42% strand | — |
| B, D, I | AMC018 GP41 | protein | 125 | 50% helix, 3% strand | — |
| H, E, F | PGV04 Fab heavy chain | protein | 123 | 9% helix, 47% strand | — |
| L, J, K | PGV04 kappa chain | protein | 101 | 3% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 66 copies · chains A, H, L, C, E, J, G, F, K
- MAN · alpha-D-mannopyranose · sugar · 24 copies · chains L, H, A, J, E, C, K, F, G
- BMA · beta-D-mannopyranose · sugar · 9 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.80 | 0.82 | 85 | empty |
| 2 | 1004 | 0.78 | 0.80 | 90 | empty |
| 3 | 1059 | 0.76 | 0.79 | 85 | empty |
| 4 | 701 | 0.74 | 0.80 | 88 | empty |
| 5 | 595 | 0.73 | 0.81 | 59 | empty |
Interfaces
27 interfaces between chains.
- A–B · 2555 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2550 Ų buried · 30 hydrogen bonds · protein-protein
- G–I · 2538 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 1027 Ų buried · 9 hydrogen bonds · protein-protein
- D–I · 1023 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 36 disulfide (N-glycosylation, disulfide).
Compared structures
- 7RSN · AMC018 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 7RSN · PDBe 7RSN
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