MolNFT v1 · #52562 · protein

X-ray structure of a dap-kinase 2-277

2W4J · Death-associated protein kinase 1: “X-ray structure of a dap-kinase 2-277”. X-ray diffraction, 2 ligands (ADP, MG), 2 pockets (best druggability 0.69). MolNFT v1 #52562 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2W4J
Type: protein
Length: 276 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Death-associated protein kinase 1
EC: 2.7.11.1
UniProt: P53355
Ligands: ADP, MG
Pockets: 2 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Death-associated protein kinase 1 (EC 2.7.11.1)	protein	276	36% helix, 20% strand	P53355

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A
MG · Magnesium ion · metal · chains A
ACT · Acetate ion · additive · chains A

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

Pockets

2 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	418	0.69	0.81	50	ADP, MG
2	104	0.37	0.74	20	empty

Compared structures

2W4J · X-ray structure of a DAP-Kinase 2-277 · 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 0.96

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
Elsewhere: RCSB PDB 2W4J · PDBe 2W4J · UniProt P53355

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