Research workbench
Crystal structure of a fragment of dc-signr (containing the carbohydrate recognition domain and two repeats of the neck).
Analyse Crystal structure of a fragment of dc-signr (containing the carbohydrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XAR
- Type
- protein
- Length
- 290 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CD209 antigen-like protein 1
- UniProt
- Q9H2X3
- Ligands
- NA
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CD209 antigen-like protein 1 | protein | 146 | 28% helix, 28% strand | Q9H2X3 |
| B | CD209 antigen-like protein 1 | protein | 144 | 26% helix, 27% strand | Q9H2X3 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.72 | 0.80 | 55 | empty |
| 2 | 114 | 0.43 | 0.78 | 24 | empty |
| 3 | 100 | 0.37 | 0.75 | 20 | empty |
| 4 | 55 | 0.29 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 782 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1XAR · Crystal Structure of a fragment of DC-SIGNR (containing the carbohydrate recognition… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H2X3 · AlphaFold monomer V2.0 prediction for C-type lectin domain family 4 member M (Q9H2X3) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q9H2X3
- Elsewhere: RCSB PDB 1XAR · PDBe 1XAR · UniProt Q9H2X3
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