Research workbench
Structure of immunoglobulin
Analyse Structure of immunoglobulin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IGY
- Type
- protein
- Length
- 1,294 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG1 intact antibody MAB61.1.3
- Ligands
- NAG, MAN, NDG, BMA, GAL, FUL, FUC
- Pockets
- 17 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | IGG1 intact antibody MAB61.1.3 | protein | 213 | 6% helix, 39% strand | — |
| B, D | IGG1 intact antibody MAB61.1.3 | protein | 434 | 7% helix, 34% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, D
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains B, D
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains B, D
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains B, D
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains B, D
- FUL · beta-L-fucopyranose · sugar · chains B
- FUC · alpha-L-fucopyranose · sugar · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.57 | 0.74 | 44 | empty |
| 2 | 199 | 0.55 | 0.79 | 23 | empty |
| 3 | 346 | 0.54 | 0.74 | 38 | empty |
| 4 | 100 | 0.47 | 0.80 | 23 | empty |
| 5 | 174 | 0.47 | 0.76 | 26 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1868 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1819 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 1444 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 182 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 46 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1IGY · Structure of immunoglobulin · the same entry in another collection · chain A against A, 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 1IGY · PDBe 1IGY
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