MolNFT v1 · #28768 · protein
Structure of the C-terminal domain of human thrombospondin-2
1YO8: “Structure of the C-terminal domain of human thrombospondin-2”. X-ray diffraction, 3 ligands (NAG, MAN, CA), 3 pockets (best druggability 0.77). MolNFT v1 #28768 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1YO8
- Type
- protein
- Length
- 621 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombospondin-2
- UniProt
- P35442
- Ligands
- NAG, MAN, CA
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombospondin-2 | protein | 621 | 6% helix, 24% strand | P35442 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- MAN · alpha-D-mannopyranose · sugar
- CA · Calcium ion · metal · 30 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.77 | 0.79 | 103 | empty |
| 2 | 133 | 0.53 | 0.82 | 26 | empty |
| 3 | 98 | 0.32 | 0.72 | 15 | CA |
Modifications
Observed in the structure: 18 disulfide, 5 modified, 4 glycan (disulfide, engineered, N-glycosylation, O-glycosylation).
Compared structures
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 P35442
- Elsewhere: RCSB PDB 1YO8 · PDBe 1YO8 · UniProt P35442
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