Research workbench
Crystal structure of human paired immunoglobulin-like type 2 receptor alpha with synthesized glycopeptide II
Analyse Crystal structure of human paired immunoglobulin-like type 2 receptor alpha… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XO2
- Type
- protein
- Length
- 254 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Paired immunoglobulin-like type 2 receptor alpha; Peptide from envelope glycoprotein B
- UniProt
- Q9UKJ1, P06437
- Ligands
- 8B9, SIA
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Paired immunoglobulin-like type 2 receptor alpha | protein | 120 | 5% helix, 51% strand | Q9UKJ1 |
| X, Y | Peptide from envelope glycoprotein B | protein | 7 | 0% helix, 0% strand | P06437 |
Ligands and binding sites
- 8B9 · 2-acetamido-2,4-dideoxy-alpha-D-xylo-hexopyranose · ligand · 2 copies · chains A, B, X, Y
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, X, B, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 529 | 0.69 | 0.79 | 67 | SIA |
| 2 | 57 | 0.29 | 0.75 | 16 | SIA |
Interfaces
5 interfaces between chains.
- A–X · 255 Ų buried · 2 hydrogen bonds · protein-protein
- B–Y · 250 Ų buried · 2 hydrogen bonds · protein-protein
- A–Y · 147 Ų buried · 2 hydrogen bonds · protein-protein
- B–X · 141 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 104 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5XO2 · Crystal structure of human paired immunoglobulin-like type 2 receptor alpha with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UKJ1 · AlphaFold monomer V2.0 prediction for paired immunoglobulin-like type 2 receptor alpha… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9UKJ1
- Every structure of UniProt P06437
- Elsewhere: RCSB PDB 5XO2 · PDBe 5XO2 · UniProt Q9UKJ1 · UniProt P06437
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