Research workbench
Human receptor nkr-P1 in glycosylated form, extracellular domain
Analyse Human receptor nkr-P1 in glycosylated form, extracellular domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MGR
- Type
- protein
- Length
- 250 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Killer cell lectin-like receptor subfamily B member 1
- UniProt
- Q12918
- Ligands
- NAG, MAN, BMA
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Killer cell lectin-like receptor subfamily B member 1 | protein | 125 | 14% helix, 34% strand | Q12918 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
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 | 352 | 0.56 | 0.75 | 45 | NAG |
| 2 | 53 | 0.26 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 588 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5MGR · Human receptor NKR-P1 in glycosylated form, extracellular domain · the same entry in another collection · chain A against A, TM-score 1.00
- Q12918 · AlphaFold monomer V2.0 prediction for killer cell lectin-like receptor subfamily B member… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q12918
- Elsewhere: RCSB PDB 5MGR · PDBe 5MGR · UniProt Q12918
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