Research workbench
BG505 SOSIP.664 trimer in complex with broadly neutralizing HIV antibodies 3BNC117 and PGT145
Analyse BG505 SOSIP.664 trimer in complex with broadly neutralizing HIV antibodies… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V8L
- Type
- protein
- Length
- 2,635 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GP120; GP41; 3BNC117 antibody, heavy chain; PGT145 antibody, heavy chain; 3BNC117…
- UniProt
- Q2N0S6
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 10 distinct chains · 22% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GP120 | protein | 450 | 15% helix, 36% strand | Q2N0S6 |
| B | GP41 | protein | 126 | 66% helix, 2% strand | Q2N0S6 |
| C | GP120 | protein | 451 | 14% helix, 36% strand | Q2N0S6 |
| D | GP120 | protein | 452 | 15% helix, 37% strand | Q2N0S6 |
| E | GP41 | protein | 124 | 68% helix, 4% strand | Q2N0S6 |
| F | GP41 | protein | 123 | 69% helix, 2% strand | Q2N0S6 |
| G, H, I | 3BNC117 antibody, heavy chain | protein | 121 | 7% helix, 45% strand | — |
| J | PGT145 antibody, heavy chain | protein | 140 | 11% helix, 59% strand | — |
| K, L, M | 3BNC117 antibody, light chain | protein | 98 | 3% helix, 44% strand | — |
| N | PGT145 antibody, light chain | protein | 112 | 3% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 106 copies · chains A, B, J, H, L, C, G, K, D, E, N, I, M, F
- MAN · alpha-D-mannopyranose · sugar · 36 copies · chains A, L, C, K, J, N, D, M
- BMA · beta-D-mannopyranose · sugar · 15 copies · chains A, L, N, K, J, D, M
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 | 0.84 | 0.85 | 113 | empty |
| 2 | 1167 | 0.80 | 0.81 | 135 | empty |
| 3 | 1082 | 0.79 | 0.81 | 116 | NAG |
| 4 | 102 | 0.77 | 0.97 | 38 | empty |
| 5 | 678 | 0.77 | 0.82 | 68 | NAG |
Interfaces
29 interfaces between chains.
- D–E · 2578 Ų buried · 29 hydrogen bonds · protein-protein
- C–F · 2553 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2511 Ų buried · 26 hydrogen bonds · protein-protein
- B–E · 1030 Ų buried · 11 hydrogen bonds · protein-protein
- J–N · 965 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 63 glycan, 41 disulfide (N-glycosylation, disulfide).
Compared structures
- 5V8L · BG505 SOSIP.664 trimer in complex with broadly neutralizing HIV antibodies 3BNC117 and… · 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 5V8L · PDBe 5V8L · UniProt Q2N0S6
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