MolNFT v1 · #108131 · protein

Leishmania major thymidine kinase in complex with AP5DT

4UXH: “Leishmania major thymidine kinase in complex with AP5DT”. X-ray diffraction, 2 ligands (T5A, ZN), 4 pockets (best druggability 0.64). MolNFT v1 #108131 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4UXH
Type: protein
Length: 337 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thymidine kinase
EC: 2.7.1.21
UniProt: Q4QC75
Ligands: T5A, ZN
Pockets: 4 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thymidine kinase (EC 2.7.1.21)	protein	173	29% helix, 26% strand	Q4QC75
B	Thymidine kinase (EC 2.7.1.21)	protein	164	29% helix, 27% strand	Q4QC75

Ligands and binding sites

T5A · P1-(5'-adenosyl)p5-(5'-thymidyl)pentaphosphate · 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	200	0.64	0.84	36	T5A
2	124	0.54	0.82	27	T5A
3	57	0.38	0.80	12	empty
4	60	0.34	0.77	14	empty

Interfaces

1 interface between chains.

A–B · 1155 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

4UXH · Leishmania major Thymidine Kinase in complex with AP5dT · the same entry in another collection · 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 Q4QC75
Elsewhere: RCSB PDB 4UXH · PDBe 4UXH · UniProt Q4QC75

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