Research workbench
Crystal structure of broad and potent HIV-1 neutralizing antibody PGT128 in complex with MAN9
Analyse Crystal structure of broad and potent HIV-1 neutralizing antibody PGT128 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TV3
- Type
- protein
- Length
- 439 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PGT128 light chain, ig lambda-2 chain C regions; PGT128 heavy chain, ig gamma-1 chain C…
- UniProt
- P0CG05, P01857
- Ligands
- AML, MAN
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | PGT128 light chain, ig lambda-2 chain C regions | protein | 205 | 7% helix, 53% strand | P0CG05 |
| H | PGT128 heavy chain, ig gamma-1 chain C region | protein | 234 | 8% helix, 51% strand | P01857 |
Ligands and binding sites
- AML · Amylamine · ligand · chains H
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains L, H
- GOL · Glycerol · additive · 4 copies · chains L, H
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 606 | 0.64 | 0.75 | 55 | GOL |
| 2 | 193 | 0.49 | 0.76 | 31 | empty |
| 3 | 62 | 0.44 | 0.83 | 19 | empty |
| 4 | 59 | 0.25 | 0.72 | 15 | empty |
Interfaces
1 interface between chains.
- L–H · 1768 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 3TV3 · Crystal structure of broad and potent HIV-1 neutralizing antibody PGT128 in complex with… · the same entry in another collection · chain L against L, 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 P0CG05
- Every structure of UniProt P01857
- Elsewhere: RCSB PDB 3TV3 · PDBe 3TV3 · UniProt P0CG05 · UniProt P01857
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