Research workbench
Structure of nk cell receptor KLRG1 bound to E-cadherin
Analyse Structure of nk cell receptor KLRG1 bound to E-cadherin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FF8
- Type
- protein
- Length
- 425 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epithelial cadherin; Killer cell lectin-like receptor subfamily G member 1
- UniProt
- P12830, O88713
- Ligands
- CA
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epithelial cadherin | protein | 101 | 4% helix, 43% strand | P12830 |
| B | Epithelial cadherin | protein | 100 | 4% helix, 42% strand | P12830 |
| C | Killer cell lectin-like receptor subfamily G member 1 | protein | 111 | 15% helix, 36% strand | O88713 |
| D | Killer cell lectin-like receptor subfamily G member 1 | protein | 113 | 15% helix, 37% strand | O88713 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 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 | 742 | 0.73 | 0.78 | 81 | empty |
| 2 | 51 | 0.33 | 0.79 | 16 | empty |
Interfaces
4 interfaces between chains.
- C–D · 712 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 585 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 584 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 368 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3FF8 · Structure of NK cell receptor KLRG1 bound to E-cadherin · the same entry in another collection · chain B against B, TM-score 1.00
- O88713 · AlphaFold monomer V2.0 prediction for killer cell lectin-like receptor subfamily G member… · a predicted model of the same protein · chain D against A, TM-score 0.96
- P12830 · AlphaFold monomer V2.0 prediction for cadherin-1 (P12830) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 P12830
- Every structure of UniProt O88713
- Elsewhere: RCSB PDB 3FF8 · PDBe 3FF8 · UniProt P12830 · UniProt O88713
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