Research workbench

X-ray structure of a dap-kinase calmodulin complex

Analyse X-ray structure of a dap-kinase calmodulin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2X0G
Type: protein
Length: 450 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.2
Source: HOMO SAPIENS
Molecule: Death-associated protein kinase 1; Calmodulin
EC: 2.7.11.1
UniProt: P53355, P62158
Ligands: CA, SO4
Pockets: 4 · best druggability 0.82

Structure

x-ray diffraction · resolution 2.2 · 2 distinct chains · 46% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Death-associated protein kinase 1 (EC 2.7.11.1)	protein	318	41% helix, 17% strand	P53355
B	Calmodulin	protein	132	58% helix, 5% strand	P62158

Ligands and binding sites

CA · Calcium ion · metal · 4 copies · chains B
SO4 · Sulfate ion · ion · 2 copies · chains A

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	939	0.82	0.84	90	empty
2	72	0.65	0.91	13	empty
3	59	0.45	0.83	11	empty
4	51	0.26	0.74	15	empty

Interfaces

1 interface between chains.

A–B · 1988 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

2X0G · X-ray structure of a dap-kinase calmodulin complex · the same entry in another collection · chain A against A, TM-score 1.00
P53355 · AlphaFold monomer V2.0 prediction for death-associated protein kinase 1 (P53355) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P53355
Every structure of UniProt P62158
Elsewhere: RCSB PDB 2X0G · PDBe 2X0G · UniProt P53355 · UniProt P62158

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