Research workbench
Crystal structure of PGT121 Fab bound to a complex-type sialylated N- glycan
Analyse Crystal structure of PGT121 Fab bound to a complex-type sialylated N- glycan in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FQC
- Type
- protein
- Length
- 433 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab heavy chain; Fab light chain
- Ligands
- TAM, NAG, MAN, BMA, GAL, SIA, FUC
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab heavy chain | protein | 227 | 8% helix, 53% strand | — |
| L | Fab light chain | protein | 206 | 7% helix, 47% strand | — |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains H
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
- GAL · beta-D-galactopyranose · sugar
- SIA · N-acetyl-alpha-neuraminic acid · sugar
- FUC · alpha-L-fucopyranose · sugar · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 764 | 0.67 | 0.75 | 61 | empty |
| 2 | 85 | 0.35 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- H–L · 1882 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4FQC · Crystal Structure of PGT121 Fab Bound to a complex-type sialylated N-glycan · the same entry in another collection · chain H against H, 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 4FQC · PDBe 4FQC
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