MolNFT v1 · #136942 · protein
BG505 SOSIP.664 trimer in complex with broadly neutralizing HIV antibodies 3BNC117 and PGT145
5V8L · GP120: “BG505 SOSIP.664 trimer in complex with broadly neutralizing HIV antibodies 3BNC117 and PGT145”. Electron microscopy, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.84). MolNFT v1 #136942 on GenesisL1: 3D…
- 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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