Research workbench
Crystal structure of human dendritic cell inhibitory receptor (dcir) C-type lectin domain in complex with biantennary glycan
Analyse Crystal structure of human dendritic cell inhibitory receptor (dcir) C-type… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B1X
- Type
- protein
- Length
- 518 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-type lectin domain family 4 member a
- UniProt
- Q9UMR7
- Ligands
- MAN, NAG, CA
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 34% 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 | 129 | 17% helix, 33% strand | Q9UMR7 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- 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 | 253 | 0.60 | 0.80 | 30 | empty |
| 2 | 71 | 0.38 | 0.78 | 22 | empty |
| 3 | 51 | 0.24 | 0.72 | 15 | empty |
Interfaces
3 interfaces between chains.
- C–D · 717 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 691 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 582 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5B1X · 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 5B1X · PDBe 5B1X · UniProt Q9UMR7
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