MolNFT v1 · #99078 · protein
Crystal structure of broadly and potently neutralizing antibody 3BNC117 in complex with HIV-1 clade C C1086 GP120
4LSV · Envelope glycoprotein GP120: “Crystal structure of broadly and potently neutralizing antibody 3BNC117 in complex with HIV-1 clade C C1086…”. X-ray diffraction, 1 ligand (NAG), 8 pockets (best druggability 0.78). MolNFT v1 #99078 on…
- PDB
- 4LSV
- Type
- protein
- Length
- 767 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120; Heavy chain of antibody 3BNC117; Light chain of antibody…
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP120 | protein | 343 | 14% helix, 34% strand | — |
| H | Heavy chain of antibody 3BNC117 | protein | 221 | 4% helix, 49% strand | — |
| L | Light chain of antibody 3BNC117 | protein | 203 | 6% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains G, L
- IMD · Imidazole · additive · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.78 | 0.82 | 75 | empty |
| 2 | 575 | 0.62 | 0.75 | 59 | empty |
| 3 | 138 | 0.54 | 0.81 | 27 | empty |
| 4 | 74 | 0.48 | 0.83 | 20 | NAG |
| 5 | 70 | 0.45 | 0.82 | 23 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1769 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 971 Ų buried · 19 hydrogen bonds · protein-protein
- G–L · 335 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 4LSV · Crystal structure of broadly and potently neutralizing antibody 3BNC117 in complex with… · the same entry in another collection · chain L against L, 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
- Elsewhere: RCSB PDB 4LSV · PDBe 4LSV
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