Research workbench

X-ray induced covalent inhibition of 14-3-3

Analyse X-ray induced covalent inhibition of 14-3-3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3RDH
Type: protein
Length: 932 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 14-3-3 protein ZETA/DELTA
UniProt: P63104
Ligands: 3RD, NI
Pockets: 9 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 80% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	14-3-3 protein ZETA/DELTA	protein	233	80% helix, 0% strand	P63104

Ligands and binding sites

3RD · 4-[(E)-{4-formyl-5-hydroxy-6-methyl-3-[(phosphonooxy)methyl]pyridin-2-yl}diazenyl]benzoic acid · ligand · 4 copies · chains A, B, C, D
NI · Nickel (II) ion · metal · 4 copies · chains A, C, B, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	951	0.75	0.78	82	empty
2	659	0.68	0.76	48	empty
3	614	0.66	0.76	48	empty
4	357	0.55	0.75	26	empty
5	330	0.55	0.75	25	empty

Interfaces

6 interfaces between chains.

B–C · 1008 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 975 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 746 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 744 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 23 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

3RDH · X-ray induced covalent inhibition of 14-3-3 · 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 D against A, TM-score 0.97

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
Elsewhere: RCSB PDB 3RDH · PDBe 3RDH · UniProt P63104

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