Research workbench
Human scavenger receptor C-type lectin carbohydrate- recognition domain.
Analyse Human scavenger receptor C-type lectin carbohydrate- recognition domain. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OX8
- Type
- protein
- Length
- 516 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Scavenger receptor with C-type lectin type I
- UniProt
- Q9BYH7
- Ligands
- ZN, CA, CL
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Scavenger receptor with C-type lectin type I | protein | 129 | 16% helix, 29% strand | Q9BYH7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 16 copies · chains A, B, C, D
- CA · Calcium ion · metal · 6 copies · chains C, D
- CL · Chloride ion · ion · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.62 | 0.78 | 42 | empty |
| 2 | 282 | 0.59 | 0.78 | 36 | empty |
| 3 | 55 | 0.28 | 0.74 | 16 | ZN |
| 4 | 58 | 0.28 | 0.74 | 16 | ZN |
Interfaces
3 interfaces between chains.
- B–D · 352 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 329 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 132 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 2OX8 · Human Scavenger Receptor C-type Lectin carbohydrate-recognition domain. · the same entry in another collection · chain A against A, 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 Q9BYH7
- Elsewhere: RCSB PDB 2OX8 · PDBe 2OX8 · UniProt Q9BYH7
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