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Binary complex of 14-3-3 zeta with ubiquitin specific protease 8 (USP8) PSER718 peptide

Analyse Binary complex of 14-3-3 zeta with ubiquitin specific protease 8 (USP8) PSER718… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6F09
Type: protein
Length: 937 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 14-3-3 protein ZETA/DELTA; Ubiquitin carboxyl-terminal hydrolase 8
EC: 3.4.19.12
UniProt: P63104, P40818
Pockets: 6 · best druggability 0.74

Structure

x-ray diffraction · 8 distinct chains · 81% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P	14-3-3 protein ZETA/DELTA	protein	227	85% helix, 0% strand	P63104
A	Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.4.19.12)	protein	7	0% helix, 0% strand	P40818
Q	14-3-3 protein ZETA/DELTA	protein	225	82% helix, 0% strand	P63104
B	Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.4.19.12)	protein	9	0% helix, 0% strand	P40818
R	14-3-3 protein ZETA/DELTA	protein	225	85% helix, 0% strand	P63104
C	Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.4.19.12)	protein	6	0% helix, 0% strand	P40818
S	14-3-3 protein ZETA/DELTA	protein	228	82% helix, 0% strand	P63104
D	Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.4.19.12)	protein	10	0% helix, 0% strand	P40818

Pockets

6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	941	0.74	0.77	95	empty
2	64	0.67	0.94	18	empty
3	420	0.65	0.78	47	empty
4	177	0.56	0.80	27	empty
5	79	0.52	0.85	19	empty

Interfaces

8 interfaces between chains.

S–D · 786 Å² buried · 19 hydrogen bonds · protein-protein
Q–B · 731 Å² buried · 18 hydrogen bonds · protein-protein
P–A · 646 Å² buried · 12 hydrogen bonds · protein-protein
R–C · 539 Å² buried · 11 hydrogen bonds · protein-protein
P–S · 312 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

6F09 · Binary complex of 14-3-3 zeta with ubiquitin specific protease 8 (USP8) pSer718 peptide · the same entry in another collection · chain D against D, TM-score 1.00
P63104 · AlphaFold monomer V2.0 prediction for 14-3-3 protein ZETA/DELTA (P63104) · a predicted model of the same protein · chain R against A, TM-score 0.99

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 P63104
Every structure of UniProt P40818
Elsewhere: RCSB PDB 6F09 · PDBe 6F09 · UniProt P63104 · UniProt P40818

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