MolNFT v1 · #146629 · protein

Spry domain-containing socs box protein 2 complexed with (gzj) VDINNN(CY3) cyclic peptide inhibitor

6DN8 · Spry domain-containing socs box protein 4: “Spry domain-containing socs box protein 2 complexed with (gzj) VDINNN(CY3) cyclic peptide inhibitor”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.75). MolNFT v1…

PDB: 6DN8
Type: protein
Length: 612 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spry domain-containing socs box protein 4; (GZJ)VDINNN(CY3) cyclic peptide inhibitor
UniProt: Q96A44
Ligands: SO4
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 5 distinct chains · 8% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spry domain-containing socs box protein 4	protein	195	8% helix, 45% strand	Q96A44
B, D	(GZJ)VDINNN(CY3) cyclic peptide inhibitor	protein	8	0% helix, 0% strand	—
C	Spry domain-containing socs box protein 4	protein	198	8% helix, 42% strand	Q96A44
E	Spry domain-containing socs box protein 4	protein	196	9% helix, 43% strand	Q96A44
F	(GZJ)VDINNN(CY3) cyclic peptide inhibitor	protein	7	0% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, C
ACT · Acetate ion · additive · 3 copies · chains A, C, E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1059	0.75	0.78	86	ACT
2	164	0.46	0.76	27	empty
3	98	0.42	0.78	18	empty

Interfaces

7 interfaces between chains.

C–E · 587 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 422 Å² buried · 7 hydrogen bonds · protein-protein
E–F · 355 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 334 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 320 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 modified (nonstandard).

Compared structures

6DN8 · SPRY domain-containing SOCS box protein 2 complexed with (GZJ)VDINNN(CY3) Cyclic peptide… · the same entry in another collection · chain F against F, 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 A 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 6DN8 · PDBe 6DN8 · UniProt Q96A44

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