Research workbench
BG505 SOSIP.V5.2 in complex with rhesus macaque Fab RM20J
Analyse BG505 SOSIP.V5.2 in complex with rhesus macaque Fab RM20J in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VO1
- Type
- protein
- Length
- 2,382 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120; Envelope glycoprotein GP41; RM20J heavy chain Fab; RM20J…
- UniProt
- Q2N0S6
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 4 distinct chains · 20% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Envelope glycoprotein GP120 | protein | 440 | 16% helix, 37% strand | Q2N0S6 |
| B, E, F | Envelope glycoprotein GP41 | protein | 129 | 59% helix, 7% strand | Q2N0S6 |
| H, G, I | RM20J heavy chain Fab | protein | 118 | 5% helix, 56% strand | — |
| L, J, K | RM20J kappa light chain | protein | 107 | 3% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 72 copies · chains A, B, C, E, D, F
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains A, C, D
- BMA · beta-D-mannopyranose · sugar · 6 copies
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 | 803 | 0.80 | 0.83 | 98 | empty |
| 2 | 1111 | 0.79 | 0.81 | 143 | empty |
| 3 | 887 | 0.73 | 0.78 | 102 | empty |
| 4 | 331 | 0.72 | 0.84 | 53 | NAG |
| 5 | 474 | 0.71 | 0.81 | 71 | NAG |
Interfaces
24 interfaces between chains.
- C–E · 2395 Ų buried · 25 hydrogen bonds · protein-protein
- D–F · 2394 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2386 Ų buried · 25 hydrogen bonds · protein-protein
- B–E · 984 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 984 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 glycan, 42 disulfide (N-glycosylation, disulfide).
Compared structures
- 6VO1 · BG505 SOSIP.v5.2 in complex with rhesus macaque Fab RM20J · 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 6VO1 · PDBe 6VO1 · UniProt Q2N0S6
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