MolNFT v1 · #41081 · protein

Active site mutant of dnk from D. melanogaster with dttp bound

2JCS · Deoxynucleoside kinase: “Active site mutant of dnk from D. melanogaster with dttp bound”. X-ray diffraction, 2 ligands (TTP, MG), 5 pockets (best druggability 0.75). MolNFT v1 #41081 on GenesisL1: 3D structure, binding sites and…

PDB: 2JCS
Type: protein
Length: 396 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Deoxynucleoside kinase
EC: 2.7.1.145
UniProt: Q9XZT6
Ligands: TTP, MG
Pockets: 5 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 52% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Deoxynucleoside kinase (EC 2.7.1.145)	protein	198	52% helix, 16% strand	Q9XZT6

Ligands and binding sites

TTP · Thymidine-5'-triphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

5 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	162	0.75	0.92	34	TTP, MG
2	147	0.74	0.92	31	TTP, MG
3	57	0.45	0.83	15	empty
4	63	0.44	0.82	13	empty
5	60	0.33	0.76	11	empty

Interfaces

1 interface between chains.

A–B · 1483 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

2JCS · Active site mutant of dNK from D. melanogaster with dTTP bound · 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 B 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 2JCS · PDBe 2JCS · UniProt Q9XZT6

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