Research workbench
Crystal structure of extracellular domain of human lectin-like transcript 1 (LLT1), the ligand for natural killer receptor-P1A
Analyse Crystal structure of extracellular domain of human lectin-like transcript 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WCO
- Type
- protein
- Length
- 344 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-type lectin domain family 2 member D
- UniProt
- Q9UHP7
- Ligands
- ZN, SO4
- Pockets
- 2 · best druggability 0.31
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C-type lectin domain family 2 member D | protein | 117 | 18% helix, 32% strand | Q9UHP7 |
| B | C-type lectin domain family 2 member D | protein | 113 | 19% helix, 33% strand | Q9UHP7 |
| C | C-type lectin domain family 2 member D | protein | 114 | 18% helix, 32% strand | Q9UHP7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 7 copies · chains A, B, C
- SO4 · Sulfate ion · ion · chains B, C
- ACT · Acetate ion · additive · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.31 | 0.74 | 16 | empty |
| 2 | 58 | 0.30 | 0.75 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 702 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 649 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 4WCO · Crystal structure of extracellular domain of human lectin-like transcript 1 (LLT1), the… · the same entry in another collection · chain A against A, 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 C 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 Q9UHP7
- Elsewhere: RCSB PDB 4WCO · PDBe 4WCO · UniProt Q9UHP7
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