MolNFT v1 · #115032 · protein
Crystal structure BG505 sosip GP140 HIV-1 env trimer bound to broadly neutralizing antibodies PGT128 and 8ANC195
5C7K · Antibody Fab PGT128 heavy chain: “Crystal structure BG505 sosip GP140 HIV-1 env trimer bound to broadly neutralizing antibodies PGT128 and…”. X-ray diffraction, 4 ligands (MAN, NAG, BMA), 17 pockets (best druggability 0.71). MolNFT…
- PDB
- 5C7K
- Type
- protein
- Length
- 1,442 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody Fab PGT128 heavy chain; Antibody Fab PGT128 light chain; Envelope glycoprotein…
- UniProt
- S6B291, C6KXN3, Q2N0S6, P01857, P01834
- Ligands
- MAN, NAG, BMA, SO4
- Pockets
- 17 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody Fab PGT128 heavy chain | protein | 230 | 1% helix, 54% strand | S6B291 |
| B | Antibody Fab PGT128 light chain | protein | 204 | 6% helix, 49% strand | C6KXN3 |
| C | Envelope glycoprotein GP120 | protein | 450 | 12% helix, 37% strand | Q2N0S6 |
| D | Envelope glycoprotein GP41 | protein | 122 | 44% helix, 6% strand | Q2N0S6 |
| E | Antibody Fab 8ANC195 heavy chain | protein | 224 | 3% helix, 51% strand | P01857 |
| F | Antibody Fab 8ANC195 light chain | protein | 212 | 6% helix, 49% strand | P01834 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 38 copies · chains E, F, A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 34 copies · chains A, C, E, D, F
- BMA · beta-D-mannopyranose · sugar · 10 copies · chains E, A, B, C, F
- SO4 · Sulfate ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.71 | 0.96 | 21 | empty |
| 2 | 575 | 0.67 | 0.77 | 57 | empty |
| 3 | 221 | 0.65 | 0.84 | 24 | empty |
| 4 | 262 | 0.65 | 0.82 | 49 | NAG |
| 5 | 228 | 0.64 | 0.83 | 32 | empty |
Interfaces
7 interfaces between chains.
- C–D · 2458 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 2001 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1818 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 855 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 601 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 glycan, 21 disulfide (disulfide, N-glycosylation, glycosylation).
Compared structures
- 5C7K · Crystal structure BG505 SOSIP gp140 HIV-1 Env trimer bound to broadly neutralizing… · the same entry in another collection · chain C against C, TM-score 1.00
- P01834 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01834) · a predicted model of the same protein · chain F against A, TM-score 0.48
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 S6B291
- Every structure of UniProt C6KXN3
- Every structure of UniProt Q2N0S6
- Every structure of UniProt P01857
- Every structure of UniProt P01834
- Elsewhere: RCSB PDB 5C7K · PDBe 5C7K · UniProt S6B291 · UniProt C6KXN3 · UniProt Q2N0S6 · UniProt P01857 · UniProt P01834
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