Research workbench
Afamin antibody fragment, N14 Fab, L1- glycosylated, crystal form I, parsimonious model
Analyse Afamin antibody fragment, N14 Fab, L1- glycosylated, crystal form I… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L9D
- Type
- protein
- Length
- 429 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mouse antibody Fab fragment, IGG1-kappa heavy chain; Mouse antibody Fab fragment…
- Ligands
- NAG, K
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Mouse antibody Fab fragment, IGG1-kappa heavy chain | protein | 215 | 8% helix, 53% strand | — |
| L | Mouse antibody Fab fragment, IGG1-kappa light chain | protein | 214 | 8% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains L
- K · Potassium ion · metal · chains H
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains H, L
- PG4 · Tetraethylene glycol · additive · 2 copies · chains H, L
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · chains H
- PGE · Triethylene glycol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 528 | 0.62 | 0.75 | 56 | PEG |
| 2 | 125 | 0.40 | 0.75 | 26 | empty |
| 3 | 71 | 0.31 | 0.74 | 18 | PG4 |
Interfaces
1 interface between chains.
- H–L · 1940 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5L9D · AFAMIN ANTIBODY FRAGMENT, N14 FAB, L1- GLYCOSYLATED, CRYSTAL FORM I, parsimonious model · 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 5L9D · PDBe 5L9D
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