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Structure of Cdc14 bound to CBK1 PxL motif

Analyse Structure of Cdc14 bound to CBK1 PxL motif in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6G84
Type: protein
Length: 742 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.47
Source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c); SYNTHETIC CONSTRUCT
Molecule: Tyrosine-protein phosphatase CDC14; CBK1
EC: 3.1.3.48
UniProt: Q00684
Ligands: CA, ZN
Pockets: 10 · best druggability 0.84

Structure

x-ray diffraction · resolution 2.47 · 4 distinct chains · 42% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tyrosine-protein phosphatase CDC14 (EC 3.1.3.48)	protein	356	44% helix, 15% strand	Q00684
D	CBK1	protein	7	0% helix, 0% strand	—
B	Tyrosine-protein phosphatase CDC14 (EC 3.1.3.48)	protein	368	41% helix, 14% strand	Q00684
C	CBK1	protein	11	0% helix, 0% strand	—

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, B
ZN · Zinc ion · metal · chains B
EDO · 1,2-ethanediol · additive · chains A

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

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	208	0.84	0.97	39	empty
2	197	0.57	0.79	23	EDO
3	187	0.57	0.80	24	empty
4	186	0.54	0.79	24	empty
5	148	0.50	0.78	21	empty

Interfaces

3 interfaces between chains.

A–B · 1786 Å² buried · 29 hydrogen bonds · protein-protein
B–C · 633 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 415 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6G84 · Structure of CDC14 bound to CBK1 pxl motif · the same entry in another collection · chain A against A, TM-score 1.00
Q00684 · AlphaFold monomer V2.0 prediction for tyrosine-protein phosphatase CDC14 (Q00684) · a predicted model of the same protein · chain A 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 Q00684
Elsewhere: RCSB PDB 6G84 · PDBe 6G84 · UniProt Q00684

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