MolNFT v1 · #146626 · protein
Spry domain-containing socs box protein 2 complexed with WDINNN(BAL) cyclic peptide inhibitor
6DN5: “Spry domain-containing socs box protein 2 complexed with WDINNN(BAL) cyclic peptide inhibitor”. X-ray diffraction, 1 ligand (SO4), 1 pocket (best druggability 0.38). MolNFT v1 #146626 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6DN5
- Type
- protein
- Length
- 201 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spry domain-containing socs box protein 2; WDINNN(BAL) cyclic peptide inhibitor
- UniProt
- Q99619
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spry domain-containing socs box protein 2 | protein | 194 | 10% helix, 41% strand | Q99619 |
| B | WDINNN(BAL) cyclic peptide inhibitor | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · 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 | 0.38 | 0.80 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 326 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 6DN5 · 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
- Q99619 · AlphaFold monomer V2.0 prediction for spry domain-containing socs box protein 2 (Q99619) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q99619
- Elsewhere: RCSB PDB 6DN5 · PDBe 6DN5 · UniProt Q99619
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