MolNFT v1 · #123698 · protein
Uncleaved prefusion optimized GP140 trimer with an engineered 10- residue HR1 turn bound to broadly neutralizing antibodies 8ANC195 and PGT128
5JSA · Broadly neutralizing antibody PGT128 heavy chain: “Uncleaved prefusion optimized GP140 trimer with an engineered 10- residue HR1 turn bound to broadly…”. X-ray diffraction, 3 ligands (MAN, NAG, BMA), 16 pockets (best druggability…
- PDB
- 5JSA
- Type
- protein
- Length
- 1,449 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Broadly neutralizing antibody PGT128 heavy chain; Broadly neutralizing antibody PGT128…
- Ligands
- MAN, NAG, BMA
- Pockets
- 16 · best druggability 0.70
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Broadly neutralizing antibody PGT128 heavy chain | protein | 230 | 1% helix, 54% strand | — |
| B | Broadly neutralizing antibody PGT128 light chain | protein | 204 | 6% helix, 49% strand | — |
| C | GP120 | protein | 447 | 13% helix, 36% strand | — |
| D | GP41 | protein | 132 | 52% helix, 5% strand | — |
| E | Broadly neutralizing antibody 8ANC195 heavy chain | protein | 224 | 3% helix, 51% strand | — |
| F | Broadly neutralizing antibody 8ANC195 light chain | protein | 212 | 6% helix, 48% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 33 copies · chains E, A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 32 copies · chains A, C, E, D, F
- BMA · beta-D-mannopyranose · sugar · 12 copies · chains E, A, B, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.70 | 0.85 | 38 | empty |
| 2 | 385 | 0.69 | 0.81 | 53 | empty |
| 3 | 655 | 0.67 | 0.76 | 67 | empty |
| 4 | 317 | 0.65 | 0.80 | 55 | NAG |
| 5 | 227 | 0.64 | 0.83 | 22 | empty |
Interfaces
7 interfaces between chains.
- C–D · 2609 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1985 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1770 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 850 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 547 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide, 19 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 5JSA · Uncleaved prefusion optimized gp140 trimer with an engineered 10-residue HR1 turn bound… · 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 5JSA · PDBe 5JSA
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