Research workbench
BG505 MD39 sosip trimer in complex with mature BG18 fragment antigen binding
Analyse BG505 MD39 sosip trimer in complex with mature BG18 fragment antigen binding in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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