Research workbench
Afamin antibody fragment, N14 Fab, L1- glycosylated, crystal form II
Analyse Afamin antibody fragment, N14 Fab, L1- glycosylated, crystal form II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L7X
- Type
- protein
- Length
- 419 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
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Mouse antibody Fab fragment, IGG1-kappa heavy chain | protein | 205 | 9% helix, 55% strand | — |
| L | Mouse antibody Fab fragment, IGG1-kappa light chain | protein | 214 | 7% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains L
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains H, L
- PG4 · Tetraethylene glycol · additive · chains H
- 1PE · Pentaethylene glycol · additive · chains H, L
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 | 361 | 0.57 | 0.76 | 47 | PEG |
| 2 | 52 | 0.33 | 0.78 | 16 | empty |
| 3 | 68 | 0.31 | 0.75 | 20 | 1PE |
| 4 | 52 | 0.26 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- H–L · 1808 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5L7X · Afamin antibody fragment, N14 Fab, L1- glycosylated, crystal form II · 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 5L7X · PDBe 5L7X
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