Research workbench
Crystal structure of clec-2 in complex with rhodocytin
Analyse Crystal structure of clec-2 in complex with rhodocytin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WWK
- Type
- protein
- Length
- 1,506 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-type lectin domain family 1 member B; Snaclec rhodocytin subunit alpha; Snaclec…
- UniProt
- Q9P126, Q9I841, Q9I840
- Pockets
- 14 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, I, L, F | C-type lectin domain family 1 member B | protein | 122 | 21% helix, 34% strand | Q9P126 |
| A, D, G | Snaclec rhodocytin subunit alpha | protein | 133 | 19% helix, 29% strand | Q9I841 |
| B, E, H, K | Snaclec rhodocytin subunit beta | protein | 123 | 20% helix, 36% strand | Q9I840 |
| J | Snaclec rhodocytin subunit alpha | protein | 127 | 11% helix, 29% strand | Q9I841 |
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.64 | 0.79 | 48 | empty |
| 2 | 273 | 0.63 | 0.81 | 45 | empty |
| 3 | 406 | 0.58 | 0.75 | 37 | empty |
| 4 | 94 | 0.56 | 0.85 | 25 | empty |
| 5 | 149 | 0.54 | 0.81 | 41 | empty |
Interfaces
17 interfaces between chains.
- J–K · 1925 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 1861 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1855 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 1775 Ų buried · 19 hydrogen bonds · protein-protein
- H–K · 629 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide (disulfide).
Compared structures
- 3WWK · Crystal structure of CLEC-2 in complex with rhodocytin · the same entry in another collection · chain F against F, TM-score 1.00
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 Q9I841
- Every structure of UniProt Q9I840
- Elsewhere: RCSB PDB 3WWK · PDBe 3WWK · UniProt Q9P126 · UniProt Q9I841 · UniProt Q9I840
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