Research workbench
Complex of human nkr-P1 and LLT1 in deglycosylated forms
Analyse Complex of human nkr-P1 and LLT1 in deglycosylated forms in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MGT
- Type
- protein
- Length
- 735 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-type lectin domain family 2 member D; Killer cell lectin-like receptor subfamily B…
- UniProt
- Q9UHP7, Q12918
- Ligands
- NAG, SO4, CL
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 16% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C-type lectin domain family 2 member D | protein | 116 | 18% helix, 32% strand | Q9UHP7 |
| B | C-type lectin domain family 2 member D | protein | 116 | 18% helix, 34% strand | Q9UHP7 |
| C | Killer cell lectin-like receptor subfamily B member 1 | protein | 127 | 14% helix, 34% strand | Q12918 |
| D, F | Killer cell lectin-like receptor subfamily B member 1 | protein | 125 | 14% helix, 33% strand | Q12918 |
| E | Killer cell lectin-like receptor subfamily B member 1 | protein | 126 | 14% helix, 34% strand | Q12918 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D, F
- CL · Chloride ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1160 | 0.73 | 0.77 | 112 | NAG, SO4 |
| 2 | 53 | 0.55 | 0.90 | 26 | empty |
| 3 | 298 | 0.55 | 0.76 | 44 | NAG |
| 4 | 95 | 0.38 | 0.76 | 24 | NAG |
| 5 | 94 | 0.38 | 0.76 | 26 | NAG |
Interfaces
6 interfaces between chains.
- B–D · 832 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 679 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 600 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 587 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 273 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 5MGT · Complex of human NKR-P1 and LLT1 in deglycosylated forms · the same entry in another collection · chain F against F, TM-score 1.00
- Q9UHP7 · AlphaFold monomer V2.0 prediction for C-type lectin domain family 2 member D (Q9UHP7) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q12918 · AlphaFold monomer V2.0 prediction for killer cell lectin-like receptor subfamily B member… · a predicted model of the same protein · chain D 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 Q9UHP7
- Every structure of UniProt Q12918
- Elsewhere: RCSB PDB 5MGT · PDBe 5MGT · UniProt Q9UHP7 · UniProt Q12918
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