MolNFT v1 · #27257 · protein
Crystal structure of a ligand-binding domain of the human polymeric ig receptor, pigr
1XED · Polymeric-immunoglobulin receptor: “Crystal structure of a ligand-binding domain of the human polymeric ig receptor, pigr”. X-ray diffraction, 1 ligand (MG), 5 pockets (best druggability 0.78). MolNFT v1 #27257 on GenesisL1: 3D…
- PDB
- 1XED
- Type
- protein
- Length
- 652 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymeric-immunoglobulin receptor
- UniProt
- P01833
- Ligands
- MG
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymeric-immunoglobulin receptor | protein | 111 | 10% helix, 46% strand | P01833 |
| B | Polymeric-immunoglobulin receptor | protein | 109 | 10% helix, 47% strand | P01833 |
| C, D | Polymeric-immunoglobulin receptor | protein | 105 | 9% helix, 49% strand | P01833 |
| E, F | Polymeric-immunoglobulin receptor | protein | 111 | 10% helix, 49% strand | P01833 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, F, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.78 | 0.84 | 83 | empty |
| 2 | 452 | 0.59 | 0.74 | 37 | empty |
| 3 | 86 | 0.39 | 0.77 | 19 | empty |
| 4 | 64 | 0.34 | 0.76 | 15 | empty |
| 5 | 109 | 0.33 | 0.72 | 24 | empty |
Interfaces
9 interfaces between chains.
- E–F · 735 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 688 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 683 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 444 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 442 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 1XED · Crystal Structure of a Ligand-Binding Domain of the Human Polymeric Ig Receptor, pIgR · the same entry in another collection · chain F against F, TM-score 1.00
- P01833 · AlphaFold monomer V2.0 prediction for polymeric immunoglobulin receptor (P01833) · a predicted model of the same protein · chain E against A, TM-score 0.98
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 1XED · PDBe 1XED · UniProt P01833
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