Research workbench
Cryo-EM structure of BG505.SOSIP.664 in complex with BF520.1 antigen binding fragment
Analyse Cryo-EM structure of BG505.SOSIP.664 in complex with BF520.1 antigen binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MN7
- Type
- protein
- Length
- 2,418 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120; Envelope glycoprotein GP41; BF520.1 Fab variable region
- UniProt
- Q2N0S6, Q2N0S7
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 3 distinct chains · 17% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Envelope glycoprotein GP120 | protein | 438 | 13% helix, 38% strand | Q2N0S6 |
| B, E, F | Envelope glycoprotein GP41 | protein | 132 | 55% helix, 2% strand | Q2N0S7 |
| G, H, I | BF520.1 Fab variable region | protein | 236 | 4% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 111 copies · chains A, B, G, C, E, I, D, F, H
- MAN · alpha-D-mannopyranose · sugar · 51 copies · chains G, A, I, C, H, D
- BMA · beta-D-mannopyranose · sugar · 30 copies · chains G, I, H
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 | 978 | 0.89 | 0.90 | 185 | empty |
| 2 | 698 | 0.74 | 0.80 | 74 | empty |
| 3 | 752 | 0.73 | 0.79 | 83 | empty |
| 4 | 745 | 0.73 | 0.79 | 78 | empty |
| 5 | 747 | 0.73 | 0.78 | 79 | NAG |
Interfaces
18 interfaces between chains.
- A–B · 2738 Ų buried · 24 hydrogen bonds · protein-protein
- C–E · 2736 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 2734 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 767 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 737 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 6MN7 · Cryo-EM structure of BG505.SOSIP.664 in complex with BF520.1 antigen binding fragment · 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 Q2N0S7
- Elsewhere: RCSB PDB 6MN7 · PDBe 6MN7 · UniProt Q2N0S6 · UniProt Q2N0S7
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