Research workbench
Crystal structure of anti-HIV antibody PGT128 in complex with a bacterially derived synthetic mimetic of MAN9.
Analyse Crystal structure of anti-HIV antibody PGT128 in complex with a bacterially… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B3D
- Type
- protein
- Length
- 442 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PGT128 Fab light chain; PGT128 Fab heavy chain
- Ligands
- MAN
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | PGT128 Fab light chain | protein | 207 | 7% helix, 52% strand | — |
| H | PGT128 Fab heavy chain | protein | 235 | 8% helix, 52% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains L, H
- EDO · 1,2-ethanediol · additive · 6 copies · chains L, H
- GOL · Glycerol · additive · 3 copies · chains L
- IPA · Isopropyl alcohol · additive · 3 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
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 669 | 0.66 | 0.75 | 60 | GOL, EDO, IPA |
| 2 | 110 | 0.44 | 0.78 | 24 | empty |
| 3 | 77 | 0.36 | 0.76 | 15 | empty |
| 4 | 78 | 0.33 | 0.75 | 21 | empty |
| 5 | 56 | 0.25 | 0.72 | 12 | empty |
Interfaces
1 interface between chains.
- L–H · 1826 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 6B3D · Crystal structure of anti-HIV antibody PGT128 in complex with a bacterially derived… · 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
- Elsewhere: RCSB PDB 6B3D · PDBe 6B3D
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