Research workbench
Crystal structure of the broadly neutralizing antibody N49P6 Fab in complex with HIV-1 Clade A/E strain 93TH057 gp120 core.
Analyse Crystal structure of the broadly neutralizing antibody N49P6 Fab in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OZ2
- Type
- protein
- Length
- 763 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.55
- Source
- Homo sapiens; Human immunodeficiency virus 1
- Molecule
- clade A/E 93TH057 HIV-1 gp120 core; N49P6 antibody Fab heavy chain; N49P6 antibody Fab…
- UniProt
- A0A0M3KKW9
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.55 · 3 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | clade A/E 93TH057 HIV-1 gp120 core | protein | 338 | 18% helix, 36% strand | A0A0M3KKW9 |
| H | N49P6 antibody Fab heavy chain | protein | 225 | 4% helix, 52% strand | — |
| L | N49P6 antibody Fab light chain | protein | 200 | 6% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains G, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 170 | 0.77 | 0.94 | 34 | empty |
| 2 | 402 | 0.74 | 0.84 | 48 | empty |
| 3 | 609 | 0.67 | 0.76 | 58 | empty |
| 4 | 52 | 0.62 | 0.93 | 16 | empty |
| 5 | 209 | 0.51 | 0.77 | 46 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1725 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 826 Ų buried · 12 hydrogen bonds · protein-protein
- G–L · 179 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 6OZ2 · Crystal structure of the broadly neutralizing antibody N49P6 Fab in complex with HIV-1… · 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 A0A0M3KKW9
- Elsewhere: RCSB PDB 6OZ2 · PDBe 6OZ2 · UniProt A0A0M3KKW9
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