Research workbench
Blood dendritic cell antigen 2 (bdca-2) complexed with methyl- mannoside
Analyse Blood dendritic cell antigen 2 (bdca-2) complexed with methyl- mannoside in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZES
- Type
- protein
- Length
- 294 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-type lectin domain family 4 member C
- UniProt
- Q8WTT0
- Ligands
- MMA, CA, MG
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | C-type lectin domain family 4 member C | protein | 147 | 16% helix, 39% strand | Q8WTT0 |
Ligands and binding sites
- MMA · methyl alpha-D-mannopyranoside · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 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 | 408 | 0.62 | 0.77 | 55 | MG |
| 2 | 88 | 0.37 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 554 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4ZES · Blood dendritic cell antigen 2 (BDCA-2) complexed with methyl-mannoside · the same entry in another collection · chain A against A, TM-score 1.00
- Q8WTT0 · AlphaFold monomer V2.0 prediction for C-type lectin domain family 4 member C (Q8WTT0) · a predicted model of the same protein · chain A 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 Q8WTT0
- Elsewhere: RCSB PDB 4ZES · PDBe 4ZES · UniProt Q8WTT0
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