Research workbench
Structure of the F-spondin domain of mindin
Analyse Structure of the F-spondin domain of mindin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D34
- Type
- protein
- Length
- 426 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spondin-2
- UniProt
- Q9BUD6
- Ligands
- NI, CA
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spondin-2 | protein | 211 | 11% helix, 37% strand | Q9BUD6 |
| B | Spondin-2 | protein | 215 | 11% helix, 37% strand | Q9BUD6 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 6 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
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 | 534 | 0.68 | 0.79 | 54 | NI |
| 2 | 406 | 0.65 | 0.79 | 50 | NI |
| 3 | 106 | 0.44 | 0.78 | 22 | empty |
| 4 | 66 | 0.35 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 771 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
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 Q9BUD6
- Elsewhere: RCSB PDB 3D34 · PDBe 3D34 · UniProt Q9BUD6
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