Research workbench
Crystal structure of SPINDLIN1 bound to compound EML405
Analyse Crystal structure of SPINDLIN1 bound to compound EML405 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JSG
- Type
- protein
- Length
- 388 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spindlin-1
- UniProt
- Q9Y657
- Ligands
- 6P9, MG, CL
- Pockets
- 9 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spindlin-1 | protein | 192 | 7% helix, 44% strand | Q9Y657 |
| B | Spindlin-1 | protein | 196 | 7% helix, 50% strand | Q9Y657 |
Ligands and binding sites
- 6P9 · [2-(phenylamino)-1,4-phenylene]bis({4-[2-(pyrrolidin-1-yl)ethyl]piperidin-1-yl}methanone) · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.51 | 0.80 | 22 | MG, CL |
| 2 | 68 | 0.48 | 0.82 | 9 | empty |
| 3 | 64 | 0.43 | 0.80 | 8 | empty |
| 4 | 69 | 0.41 | 0.79 | 17 | empty |
| 5 | 52 | 0.33 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 289 Ų buried · 9 hydrogen bonds · protein-protein
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 Q9Y657
- Elsewhere: RCSB PDB 5JSG · PDBe 5JSG · UniProt Q9Y657
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