Research workbench
BG505 SOSIP.664 trimer in complex with broadly neutralizing HIV antibody 3BNC117
Analyse BG505 SOSIP.664 trimer in complex with broadly neutralizing HIV antibody 3BNC117 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V8M
- Type
- protein
- Length
- 2,376 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GP120; GP41; Antibody 3BNC117, heavy chain; Antibody 3BNC117, light chain
- UniProt
- Q2N0S6
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, G | GP120 | protein | 444 | 15% helix, 38% strand | Q2N0S6 |
| B, I, J | GP41 | protein | 129 | 63% helix, 2% strand | Q2N0S6 |
| H, R, S | Antibody 3BNC117, heavy chain | protein | 121 | 7% helix, 46% strand | — |
| L, T, U | Antibody 3BNC117, light chain | protein | 98 | 3% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 99 copies · chains A, B, H, F, L, I, R, G, T, J, S, U
- MAN · alpha-D-mannopyranose · sugar · 39 copies · chains A, L, F, T, G, U
- BMA · beta-D-mannopyranose · sugar · 15 copies · chains A, L, F, T, G, U
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 | 980 | 0.82 | 0.83 | 111 | NAG |
| 2 | 1055 | 0.81 | 0.82 | 121 | NAG |
| 3 | 1056 | 0.81 | 0.82 | 107 | empty |
| 4 | 998 | 0.80 | 0.82 | 106 | NAG |
| 5 | 941 | 0.75 | 0.78 | 97 | empty |
Interfaces
24 interfaces between chains.
- F–I · 2606 Ų buried · 30 hydrogen bonds · protein-protein
- G–J · 2605 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2603 Ų buried · 30 hydrogen bonds · protein-protein
- F–R · 940 Ų buried · 19 hydrogen bonds · protein-protein
- A–H · 940 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 5V8M · BG505 SOSIP.664 trimer in complex with broadly neutralizing HIV antibody 3BNC117 · 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 5V8M · PDBe 5V8M · UniProt Q2N0S6
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