Research workbench
Crystal structure of the human polymeric ig receptor (pigr) ectodomain
Analyse Crystal structure of the human polymeric ig receptor (pigr) ectodomain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D4K
- Type
- protein
- Length
- 1,075 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymeric immunoglobulin receptor
- UniProt
- P01833
- Ligands
- NAG, FUC, SO4
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymeric immunoglobulin receptor | protein | 539 | 6% helix, 47% strand | P01833 |
| B | Polymeric immunoglobulin receptor | protein | 536 | 6% helix, 48% strand | P01833 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 516 | 0.77 | 0.84 | 42 | empty |
| 2 | 350 | 0.55 | 0.74 | 38 | SO4 |
| 3 | 160 | 0.54 | 0.80 | 28 | empty |
| 4 | 166 | 0.53 | 0.80 | 33 | empty |
| 5 | 320 | 0.52 | 0.74 | 36 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1049 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- P01833 · AlphaFold monomer V2.0 prediction for polymeric immunoglobulin receptor (P01833) · a predicted model of the same protein · chain A against A, TM-score 0.44
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P01833
- Elsewhere: RCSB PDB 5D4K · PDBe 5D4K · UniProt P01833
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