Research workbench
SPRY domain-containing SOCS box protein 2 complexed with WDINNN(BAL) Cyclic peptide inhibitor
Analyse SPRY domain-containing SOCS box protein 2 complexed with WDINNN(BAL) Cyclic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DN7
- Type
- protein
- Length
- 404 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.4
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- SPRY domain-containing SOCS box protein 4; WDINNN(BAL) Cyclic peptide inhibitor
- UniProt
- Q96A44
- Ligands
- CL
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · resolution 1.4 · 3 distinct chains · 8% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SPRY domain-containing SOCS box protein 4 | protein | 201 | 8% helix, 42% strand | Q96A44 |
| B, D | WDINNN(BAL) Cyclic peptide inhibitor | protein | 7 | 0% helix, 0% strand | — |
| C | SPRY domain-containing SOCS box protein 4 | protein | 189 | 8% helix, 44% strand | Q96A44 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.72 | 0.78 | 58 | empty |
| 2 | 89 | 0.44 | 0.80 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–C · 406 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 323 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 323 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 6DN7 · Spry domain-containing socs box protein 2 complexed with WDINNN(BAL) cyclic peptide… · the same entry in another collection · chain A against A, TM-score 1.00
- Q96A44 · AlphaFold monomer V2.0 prediction for spry domain-containing socs box protein 4 (Q96A44) · a predicted model of the same protein · chain C against A, TM-score 1.00
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 Q96A44
- Elsewhere: RCSB PDB 6DN7 · PDBe 6DN7 · UniProt Q96A44
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