MolNFT v1 · #146371 · protein
BG505 MD39 sosip trimer in complex with mature BG18 fragment antigen binding
6DFG · Envelope glycoprotein GP160: “BG505 MD39 sosip trimer in complex with mature BG18 fragment antigen binding”. Electron microscopy, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.78). MolNFT v1 #146371 on GenesisL1: 3D…
- PDB
- 6DFG
- Type
- protein
- Length
- 2,355 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; Mature BG18 fragment antigen binding heavy chain; Mature…
- UniProt
- Q2N0S6, Q2N0S8
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 4 distinct chains · 13% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Envelope glycoprotein GP160 | protein | 435 | 12% helix, 34% strand | Q2N0S6 |
| B, E, F | Envelope glycoprotein GP160 | protein | 115 | 35% helix, 5% strand | Q2N0S8 |
| H, G, I | Mature BG18 fragment antigen binding heavy chain | protein | 129 | 2% helix, 53% strand | — |
| L, J, K | Mature BG18 fragment antigen binding light chain | protein | 106 | 4% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 78 copies · chains A, H, C, G, D, I, L, J, K
- MAN · alpha-D-mannopyranose · sugar · 42 copies · chains A, H, L, C, G, J, D, I, K
- BMA · beta-D-mannopyranose · sugar · 15 copies · chains H, G, I
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 | 232 | 0.78 | 0.91 | 43 | empty |
| 2 | 225 | 0.78 | 0.91 | 40 | NAG |
| 3 | 229 | 0.76 | 0.90 | 37 | NAG |
| 4 | 80 | 0.76 | 0.98 | 24 | empty |
| 5 | 79 | 0.76 | 0.98 | 26 | empty |
Interfaces
21 interfaces between chains.
- C–E · 2064 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 2054 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 2038 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 939 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 923 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 6DFG · BG505 MD39 SOSIP trimer in complex with mature BG18 fragment antigen binding · 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 Q2N0S6
- Every structure of UniProt Q2N0S8
- Elsewhere: RCSB PDB 6DFG · PDBe 6DFG · UniProt Q2N0S6 · UniProt Q2N0S8
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