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Crystal structure of drosophila deoxyribonucleoside kinase

Analyse Crystal structure of drosophila deoxyribonucleoside kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1J90
Type: protein
Length: 386 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Deoxyribonucleoside kinase
UniProt: Q9XZT6
Ligands: DCZ, SO4
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 52% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Deoxyribonucleoside kinase	protein	195	52% helix, 15% strand	Q9XZT6
B	Deoxyribonucleoside kinase	protein	191	52% helix, 15% strand	Q9XZT6

Ligands and binding sites

DCZ · 2'-deoxycytidine · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	160	0.72	0.90	33	SO4, DCZ
2	174	0.70	0.88	31	SO4, DCZ
3	171	0.52	0.79	24	empty
4	86	0.36	0.75	14	empty

Interfaces

1 interface between chains.

A–B · 1235 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

1J90 · Crystal Structure of Drosophila Deoxyribonucleoside Kinase · the same entry in another collection · chain A against A, TM-score 1.00
Q9XZT6 · AlphaFold monomer V2.0 prediction for deoxynucleoside kinase (Q9XZT6) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q9XZT6
Elsewhere: RCSB PDB 1J90 · PDBe 1J90 · UniProt Q9XZT6

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