Research workbench
Crystal structure of clec-2 in complex with O-glycosylated podoplanin
Analyse Crystal structure of clec-2 in complex with O-glycosylated podoplanin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WSR
- Type
- protein
- Length
- 261 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-type lectin domain family 1 member B; Peptide from podoplanin
- UniProt
- Q9P126, Q86YL7
- Ligands
- A2G, GAL, SIA
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | C-type lectin domain family 1 member B | protein | 120 | 22% helix, 35% strand | Q9P126 |
| C | Peptide from podoplanin | protein | 10 | 0% helix, 0% strand | Q86YL7 |
| D | Peptide from podoplanin | protein | 11 | 0% helix, 0% strand | Q86YL7 |
Ligands and binding sites
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 2 copies · chains A, C, D, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, C, D, 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 | 210 | 0.51 | 0.76 | 27 | SIA |
| 2 | 100 | 0.40 | 0.77 | 17 | SIA |
Interfaces
5 interfaces between chains.
- B–D · 327 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 323 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 154 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 110 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 100 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 2 glycan (disulfide, O-glycosylation).
Compared structures
- 3WSR · Crystal structure of CLEC-2 in complex with O-glycosylated podoplanin · the same entry in another collection · chain D against D, TM-score 1.00
- Q9P126 · AlphaFold monomer V2.0 prediction for C-type lectin domain family 1 member B (Q9P126) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q86YL7 · AlphaFold monomer V2.0 prediction for podoplanin (Q86YL7) · a predicted model of the same protein · chain D against A, TM-score 0.32
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 Q9P126
- Every structure of UniProt Q86YL7
- Elsewhere: RCSB PDB 3WSR · PDBe 3WSR · UniProt Q9P126 · UniProt Q86YL7
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