Research workbench
Crystal structure of broadly neutralizing antibody N49P6 Fab in complex with HIV-1 BG505 SOSIP.664 env trimer ectodomain.
Analyse Crystal structure of broadly neutralizing antibody N49P6 Fab in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OZ4
- Type
- protein
- Length
- 996 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; Envelope glycoprotein GP41; N49P6 antibody Fab heavy chain…
- UniProt
- Q2N0S6
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP160 | protein | 449 | 13% helix, 37% strand | Q2N0S6 |
| B | Envelope glycoprotein GP41 | protein | 122 | 48% helix, 3% strand | Q2N0S6 |
| H | N49P6 antibody Fab heavy chain | protein | 225 | 3% helix, 47% strand | — |
| L | N49P6 antibody light chain | protein | 200 | 8% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 31 copies · chains G, H, L, B
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains H
- MAN · alpha-D-mannopyranose · sugar · 5 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.79 | 0.96 | 34 | empty |
| 2 | 280 | 0.77 | 0.89 | 42 | NAG |
| 3 | 78 | 0.75 | 0.97 | 28 | empty |
| 4 | 149 | 0.71 | 0.90 | 36 | empty |
| 5 | 640 | 0.70 | 0.78 | 73 | empty |
Interfaces
4 interfaces between chains.
- G–B · 2332 Ų buried · 17 hydrogen bonds · protein-protein
- H–L · 1777 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 1095 Ų buried · 29 hydrogen bonds · protein-protein
- G–L · 193 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 19 glycan, 15 disulfide (N-glycosylation, disulfide).
Compared structures
- 6OZ4 · Crystal structure of broadly neutralizing antibody N49P6 Fab in complex with HIV-1 BG505… · the same entry in another collection · chain G against G, 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 6OZ4 · PDBe 6OZ4 · UniProt Q2N0S6
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