Research workbench
Crystal structure of SPINDLIN1 bound to spindoc DOCPEP3
Analyse Crystal structure of SPINDLIN1 bound to spindoc DOCPEP3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E9M
- Type
- protein
- Length
- 448 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spindlin-1; Peptide from spindlin interactor and repressor of chromatin-binding protein
- UniProt
- Q9Y657, Q9BUA3
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spindlin-1 | protein | 199 | 7% helix, 47% strand | Q9Y657 |
| B, D | Peptide from spindlin interactor and repressor of chromatin-binding protein | protein | 26 | 0% helix, 31% strand | Q9BUA3 |
| C | Spindlin-1 | protein | 197 | 7% helix, 48% strand | Q9Y657 |
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 | 256 | 0.61 | 0.80 | 35 | empty |
| 2 | 390 | 0.60 | 0.76 | 53 | empty |
| 3 | 51 | 0.37 | 0.80 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1214 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1193 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 657 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7E9M · Crystal Structure of Spindlin1 bound to SPINDOC Docpep3 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y657 · AlphaFold monomer V2.0 prediction for spindlin-1 (Q9Y657) · a predicted model of the same protein · chain A against A, TM-score 0.94
- Q9BUA3 · AlphaFold monomer V2.0 prediction for spindlin interactor and repressor of… · a predicted model of the same protein · chain B against A, TM-score 0.20
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
- Every structure of UniProt Q9BUA3
- Elsewhere: RCSB PDB 7E9M · PDBe 7E9M · UniProt Q9Y657 · UniProt Q9BUA3
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