Research workbench
Human receptor nkr-P1 in deglycosylated form, extracellular domain
Analyse Human receptor nkr-P1 in deglycosylated 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
- 5MGS
- Type
- protein
- Length
- 1,005 residues
- Chains
- 8
- 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
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 15% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, G | Killer cell lectin-like receptor subfamily B member 1 | protein | 124 | 15% helix, 35% strand | Q12918 |
| B | Killer cell lectin-like receptor subfamily B member 1 | protein | 128 | 14% helix, 34% strand | Q12918 |
| C | Killer cell lectin-like receptor subfamily B member 1 | protein | 126 | 17% helix, 34% strand | Q12918 |
| D, E | Killer cell lectin-like receptor subfamily B member 1 | protein | 125 | 14% helix, 34% strand | Q12918 |
| H | Killer cell lectin-like receptor subfamily B member 1 | protein | 129 | 14% helix, 35% strand | Q12918 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.74 | 0.78 | 94 | NAG |
| 2 | 789 | 0.69 | 0.76 | 67 | NAG |
| 3 | 344 | 0.60 | 0.77 | 45 | NAG |
| 4 | 198 | 0.60 | 0.81 | 34 | empty |
| 5 | 418 | 0.60 | 0.76 | 48 | NAG |
Interfaces
11 interfaces between chains.
- E–H · 978 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 593 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 585 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 570 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 534 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 16 glycan (disulfide, N-glycosylation).
Compared structures
- 5MGS · Human receptor NKR-P1 in deglycosylated form, extracellular domain · the same entry in another collection · chain H against H, 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 C 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 Q12918
- Elsewhere: RCSB PDB 5MGS · PDBe 5MGS · UniProt Q12918
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