MolNFT v1 · #125413 · protein
Afamin antibody fragment, N14 Fab, L1- glycosilated, crystal form I, non-parsimonious model
5L88 · Anti-afamin antibody N14, Fab fragment, heavy chain: “Afamin antibody fragment, N14 Fab, L1- glycosilated, crystal form I, non-parsimonious model”. X-ray diffraction, 3 ligands (NAG, FUC, K), 3 pockets (best druggability 0.62).…
- PDB
- 5L88
- Type
- protein
- Length
- 432 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-afamin antibody N14, Fab fragment, heavy chain; Anti-afamin antibody N14, Fab…
- Ligands
- NAG, FUC, 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 | Anti-afamin antibody N14, Fab fragment, heavy chain | protein | 217 | 8% helix, 53% strand | — |
| L | Anti-afamin antibody N14, Fab fragment, light chain | protein | 215 | 8% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains L
- FUC · alpha-L-fucopyranose · sugar · chains L
- K · Potassium ion · metal · chains H
- PGE · Triethylene glycol · additive · 5 copies · chains H, L
- PG4 · Tetraethylene glycol · additive · 4 copies · chains H, L
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains H, L
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · 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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.62 | 0.75 | 56 | PEG, PGE |
| 2 | 209 | 0.52 | 0.77 | 33 | empty |
| 3 | 100 | 0.37 | 0.75 | 20 | PG4 |
Interfaces
1 interface between chains.
- H–L · 1969 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5L88 · AFAMIN ANTIBODY FRAGMENT, N14 FAB, L1- GLYCOSILATED, CRYSTAL FORM I, non-parsimonious… · 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 5L88 · PDBe 5L88
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