MolNFT v1 · #159719 · protein
Crystal structure of broadly neutralizing antibody N49P9.1 Fab in complex with HIV-1 clade A/E strain 93TH057 GP120 core
6OZ3 · Clade A/E 93TH057 HIV-1 GP120 core: “Crystal structure of broadly neutralizing antibody N49P9.1 Fab in complex with HIV-1 clade A/E strain 93TH057…”. X-ray diffraction, 2 ligands (NAG, NA), 11 pockets (best druggability 0.74).…
- PDB
- 6OZ3
- Type
- protein
- Length
- 733 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clade A/E 93TH057 HIV-1 GP120 core; N49P9.1 antibody Fab heavy chain; N49P9.1 antibody…
- UniProt
- A0A0M3KKW9
- Ligands
- NAG, NA
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Clade A/E 93TH057 HIV-1 GP120 core | protein | 319 | 16% helix, 30% strand | A0A0M3KKW9 |
| H | N49P9.1 antibody Fab heavy chain | protein | 214 | 3% helix, 45% strand | — |
| L | N49P9.1 antibody Fab light chain | protein | 200 | 5% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains G, L
- NA · Sodium ion · metal · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 478 | 0.74 | 0.83 | 56 | empty |
| 2 | 598 | 0.66 | 0.76 | 58 | empty |
| 3 | 108 | 0.62 | 0.87 | 24 | NAG |
| 4 | 294 | 0.61 | 0.79 | 31 | empty |
| 5 | 135 | 0.55 | 0.82 | 23 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1467 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 835 Ų buried · 16 hydrogen bonds · protein-protein
- G–L · 280 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 6OZ3 · Crystal structure of broadly neutralizing antibody N49P9.1 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 6OZ3 · PDBe 6OZ3 · UniProt A0A0M3KKW9
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