MolNFT v1 · #47216 · protein

Human thymidine kinase 1 in complex with TP4A

2ORV: “Human thymidine kinase 1 in complex with TP4A”. X-ray diffraction, 2 ligands (4TA, ZN), 4 pockets (best druggability 0.64). MolNFT v1 #47216 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2ORV
Type: protein
Length: 323 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thymidine kinase
EC: 2.7.1.21
UniProt: P04183
Ligands: 4TA, ZN
Pockets: 4 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thymidine kinase (EC 2.7.1.21)	protein	163	28% helix, 27% strand	P04183
B	Thymidine kinase (EC 2.7.1.21)	protein	160	28% helix, 28% strand	P04183

Ligands and binding sites

4TA · P1-(5'-adenosyl)p4-(5'-(2'-deoxy-thymidyl))tetraphosphate · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	173	0.64	0.85	32	4TA
2	122	0.61	0.86	28	4TA
3	104	0.39	0.76	17	empty
4	71	0.37	0.78	18	empty

Interfaces

1 interface between chains.

A–B · 1245 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

2ORV · human Thymidine Kinase 1 in complex with TP4A · the same entry in another collection · chain A against A, 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 0.99

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 2ORV · PDBe 2ORV · UniProt P04183

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