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The structure of the CA2+-binding, glycosylated F-spondin domain of F- spondin, a C2-domain variant from extracellular matrix
Analyse The structure of the CA2+-binding, glycosylated F-spondin domain of F- spondin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q13
- Type
- protein
- Length
- 236 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spondin-1
- UniProt
- Q9HCB6
- Ligands
- NAG, BMA, CA, SO4
- Pockets
- 1 · best druggability 0.35
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spondin-1 | protein | 236 | 8% helix, 33% strand | Q9HCB6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.35 | 0.79 | 17 | CA |
Modifications
Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3Q13 · The Structure of the Ca2+-binding, Glycosylated F-spondin Domain of F-spondin, A… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HCB6 · AlphaFold monomer V2.0 prediction for spondin-1 (Q9HCB6) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9HCB6
- Elsewhere: RCSB PDB 3Q13 · PDBe 3Q13 · UniProt Q9HCB6
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