Research workbench
BG505 SOSIP.V4.1 in complex with rhesus macaque Fab RM20F
Analyse BG505 SOSIP.V4.1 in complex with rhesus macaque Fab RM20F in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VN0
- Type
- protein
- Length
- 2,364 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; Envelope glycoprotein GP41; RM20F Fab heavy chain; RM20F…
- UniProt
- Q2N0S6
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 4 distinct chains · 20% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Envelope glycoprotein GP160 | protein | 427 | 15% helix, 40% strand | Q2N0S6 |
| B, E, F | Envelope glycoprotein GP41 | protein | 129 | 64% helix, 5% strand | Q2N0S6 |
| H, G, I | RM20F Fab heavy chain | protein | 125 | 7% helix, 47% strand | — |
| L, J, K | RM20F kappa chain | protein | 107 | 3% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 87 copies · chains A, B, H, D, C, E, G, F, I
- MAN · alpha-D-mannopyranose · sugar · 12 copies · chains B, A, E, C, F, D
- BMA · beta-D-mannopyranose · sugar · 6 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 | 581 | 0.78 | 0.84 | 65 | empty |
| 2 | 863 | 0.74 | 0.78 | 101 | empty |
| 3 | 707 | 0.74 | 0.79 | 80 | empty |
| 4 | 845 | 0.73 | 0.78 | 93 | empty |
| 5 | 820 | 0.73 | 0.78 | 92 | empty |
Interfaces
27 interfaces between chains.
- D–F · 2784 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 2779 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2765 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 967 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 966 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 6VN0 · BG505 SOSIP.v4.1 in complex with rhesus macaque Fab RM20F · 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
- Elsewhere: RCSB PDB 6VN0 · PDBe 6VN0 · UniProt Q2N0S6
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