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Crystal structure of human Fab PG16, a broadly reactive and potent HIV-1 neutralizing antibody
Analyse Crystal structure of human Fab PG16, a broadly reactive and potent HIV-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MUG
- Type
- protein
- Length
- 2,704 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody PG16 light chain; Antibody PG16 heavy chain
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | Antibody PG16 light chain | protein | 212 | 6% helix, 50% strand | — |
| B, D, H, J | Antibody PG16 heavy chain | protein | 239 | 8% helix, 52% strand | — |
| E | Antibody PG16 light chain | protein | 211 | 6% helix, 50% strand | — |
| F, L | Antibody PG16 heavy chain | protein | 238 | 5% helix, 53% strand | — |
| I | Antibody PG16 light chain | protein | 213 | 7% helix, 50% strand | — |
| K | Antibody PG16 light chain | protein | 212 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains C, E, I, K, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 864 | 0.76 | 0.80 | 90 | empty |
| 2 | 553 | 0.75 | 0.82 | 69 | empty |
| 3 | 516 | 0.74 | 0.83 | 67 | empty |
| 4 | 931 | 0.72 | 0.77 | 85 | empty |
| 5 | 820 | 0.71 | 0.77 | 79 | empty |
Interfaces
22 interfaces between chains.
- K–L · 1873 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1866 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 1841 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1799 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1790 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 13 modified, 3 glycan (disulfide, cyclization, sulfation, N-glycosylation).
Compared structures
- 3MUG · Crystal structure of human Fab PG16, a broadly reactive and potent HIV-1 neutralizing… · 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
- Elsewhere: RCSB PDB 3MUG · PDBe 3MUG
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