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Crystal structure of thymidylate kinase from thermus thermophilus HB8

Analyse Crystal structure of thymidylate kinase from thermus thermophilus HB8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5X7J
Type: protein
Length: 384 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thymidylate kinase
EC: 2.7.4.9
UniProt: Q5SHX3
Ligands: CA, CL
Pockets: 2 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 53% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thymidylate kinase (EC 2.7.4.9)	protein	187	56% helix, 15% strand	Q5SHX3
B	Thymidylate kinase (EC 2.7.4.9)	protein	197	51% helix, 14% strand	Q5SHX3

Ligands and binding sites

CA · Calcium ion · metal · 10 copies · chains A, B
CL · Chloride ion · ion · 10 copies · chains A, B
EDO · 1,2-ethanediol · additive · 4 copies · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	203	0.52	0.77	23	empty
2	58	0.38	0.80	15	CL

Interfaces

1 interface between chains.

A–B · 997 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5X7J · Crystal structure of thymidylate kinase from thermus thermophilus HB8 · the same entry in another collection · chain B against B, TM-score 1.00
Q5SHX3 · AlphaFold monomer V2.0 prediction for thymidylate kinase (Q5SHX3) · 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 Q5SHX3
Elsewhere: RCSB PDB 5X7J · PDBe 5X7J · UniProt Q5SHX3

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