Research workbench
BG505 SOSIP.V5.2 in complex with VRC40.01 and RM19R fabs
Analyse BG505 SOSIP.V5.2 in complex with VRC40.01 and RM19R fabs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LG6
- Type
- protein
- Length
- 3,153 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120; VRC40.01 Fab heavy chain; VRC40.01 Fab kappa light chain…
- UniProt
- Q2N0S6
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 15% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F | Envelope glycoprotein GP120 | protein | 450 | 14% helix, 40% strand | Q2N0S6 |
| H, O, P | VRC40.01 Fab heavy chain | protein | 123 | 2% helix, 49% strand | — |
| L, Q, R | VRC40.01 Fab kappa light chain | protein | 107 | 3% helix, 50% strand | — |
| B, G, I | Envelope glycoprotein GP41 | protein | 146 | 57% helix, 6% strand | Q2N0S6 |
| D, M, N | RM19R Fab kappa light chain | protein | 105 | 3% helix, 50% strand | — |
| C, J, K | RM19R Fab heavy chain | protein | 120 | 5% helix, 58% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 99 copies · chains A, B, H, E, G, O, F, I, P, D, M, N
- MAN · alpha-D-mannopyranose · sugar · 24 copies · chains A, L, H, E, Q, O, F, R, P
- BMA · beta-D-mannopyranose · sugar · 9 copies · chains H, L, O, Q, P, R
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains B, 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 | 569 | 0.82 | 0.88 | 65 | empty |
| 2 | 698 | 0.79 | 0.83 | 90 | NAG |
| 3 | 767 | 0.79 | 0.82 | 86 | NAG |
| 4 | 702 | 0.78 | 0.83 | 83 | empty |
| 5 | 667 | 0.78 | 0.83 | 80 | empty |
Interfaces
48 interfaces between chains.
- F–I · 2878 Ų buried · 23 hydrogen bonds · protein-protein
- E–G · 2877 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2870 Ų buried · 23 hydrogen bonds · protein-protein
- B–I · 1159 Ų buried · 8 hydrogen bonds · protein-protein
- G–I · 1155 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 glycan, 48 disulfide (N-glycosylation, disulfide).
Compared structures
- 7LG6 · BG505 SOSIP.v5.2 in complex with VRC40.01 and RM19R Fabs · 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 7LG6 · PDBe 7LG6 · UniProt Q2N0S6
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