MolNFT v1 · #27171 · protein

Crystal structure of human thymidine kinase 1

1XBT · Thymidine kinase, cytosolic: “Crystal structure of human thymidine kinase 1”. X-ray diffraction, 3 ligands (TTP, ZN, MG), 14 pockets (best druggability 0.81). MolNFT v1 #27171 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1XBT
Type: protein
Length: 1,289 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thymidine kinase, cytosolic
EC: 2.7.1.21
UniProt: P04183
Ligands: TTP, ZN, MG
Pockets: 14 · best druggability 0.81

Structure

x-ray diffraction · 5 distinct chains · 29% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, E	Thymidine kinase, cytosolic (EC 2.7.1.21)	protein	160	29% helix, 26% strand	P04183
D	Thymidine kinase, cytosolic (EC 2.7.1.21)	protein	162	29% helix, 27% strand	P04183
F	Thymidine kinase, cytosolic (EC 2.7.1.21)	protein	161	29% helix, 27% strand	P04183
G	Thymidine kinase, cytosolic (EC 2.7.1.21)	protein	165	28% helix, 28% strand	P04183
H	Thymidine kinase, cytosolic (EC 2.7.1.21)	protein	161	29% helix, 29% strand	P04183

Ligands and binding sites

TTP · Thymidine-5'-triphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
ZN · Zinc ion · metal · 8 copies · chains A, C, B, D, E, F, H, G
MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1118	0.81	0.83	114	empty
2	996	0.81	0.83	107	empty
3	742	0.73	0.79	79	empty
4	299	0.70	0.84	41	MG, TTP
5	318	0.67	0.82	39	MG, TTP

Interfaces

15 interfaces between chains.

F–H · 1261 Å² buried · 28 hydrogen bonds · protein-protein
A–C · 1261 Å² buried · 27 hydrogen bonds · protein-protein
E–G · 1257 Å² buried · 27 hydrogen bonds · protein-protein
B–D · 1254 Å² buried · 27 hydrogen bonds · protein-protein
E–F · 851 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1XBT · Crystal Structure of Human Thymidine Kinase 1 · the same entry in another collection · chain H against H, TM-score 1.00
P04183 · AlphaFold monomer V2.0 prediction for thymidine kinase, cytosolic (P04183) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P04183
Elsewhere: RCSB PDB 1XBT · PDBe 1XBT · UniProt P04183

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