MolNFT v2 · #114373 · protein
Crystal structure of human dendritic cell inhibitory receptor (DCIR) C-type lectin domain in ligand-free form
5B1W · C-type lectin domain family 4 member A: “Crystal structure of human dendritic cell inhibitory receptor (DCIR) C-type lectin domain in ligand-free form”. X-ray diffraction at 3.05, 1 ligand (CA), 3 pockets (best druggability 0.55).…
- PDB
- 5B1W
- Type
- protein
- Length
- 516 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.05
- Source
- Homo sapiens
- Molecule
- C-type lectin domain family 4 member A
- UniProt
- Q9UMR7
- Ligands
- CA
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · resolution 3.05 · 2 distinct chains · 15% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | C-type lectin domain family 4 member A | protein | 130 | 16% helix, 34% strand | Q9UMR7 |
| C, D | C-type lectin domain family 4 member A | protein | 128 | 13% helix, 31% strand | Q9UMR7 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.55 | 0.78 | 27 | empty |
| 2 | 112 | 0.49 | 0.80 | 34 | empty |
| 3 | 62 | 0.30 | 0.75 | 13 | empty |
Interfaces
3 interfaces between chains.
- C–D · 728 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 717 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 574 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5B1W · Crystal structure of human dendritic cell inhibitory receptor (dcir) C-type lectin domain… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9UMR7 · AlphaFold monomer V2.0 prediction for C-type lectin domain family 4 member a (Q9UMR7) · a predicted model of the same protein · chain A 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 Q9UMR7
- Elsewhere: RCSB PDB 5B1W · PDBe 5B1W · UniProt Q9UMR7
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