MolNFT v1 · #10096 · protein
Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 ångströms
1IGF · IGG1-kappa B13I2 Fab (light chain): “Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 ångströms”. X-ray diffraction, 1 ligand (NAG), 14 pockets (best druggability 0.54). MolNFT v1 #10096 on…
- PDB
- 1IGF
- Type
- protein
- Length
- 874 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG1-kappa B13I2 Fab (light chain); IGG1-kappa B13I2 Fab (heavy chain)
- Ligands
- NAG
- Pockets
- 14 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M | IGG1-kappa B13I2 Fab (light chain) | protein | 219 | 6% helix, 50% strand | — |
| H, J | IGG1-kappa B13I2 Fab (heavy chain) | protein | 218 | 7% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.54 | 0.74 | 47 | empty |
| 2 | 139 | 0.45 | 0.77 | 22 | empty |
| 3 | 87 | 0.45 | 0.80 | 15 | empty |
| 4 | 80 | 0.44 | 0.80 | 17 | empty |
| 5 | 131 | 0.43 | 0.76 | 25 | empty |
Interfaces
4 interfaces between chains.
- M–J · 1923 Ų buried · 20 hydrogen bonds · protein-protein
- L–H · 1833 Ų buried · 18 hydrogen bonds · protein-protein
- L–J · 520 Ų buried · 9 hydrogen bonds · protein-protein
- L–M · 326 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 1IGF · Crystal structures of an antibody to a peptide and its complex with peptide antigen at… · 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 1IGF · PDBe 1IGF
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