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Thermotoga maritima thymidine kinase in the apo form

Analyse Thermotoga maritima thymidine kinase in the apo form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2QPO
Type: protein
Length: 602 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thymidine kinase
EC: 2.7.1.21
UniProt: Q9WYN2
Ligands: ZN, SO4
Pockets: 6 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thymidine kinase (EC 2.7.1.21)	protein	153	32% helix, 31% strand	Q9WYN2
B	Thymidine kinase (EC 2.7.1.21)	protein	150	33% helix, 31% strand	Q9WYN2
C	Thymidine kinase (EC 2.7.1.21)	protein	148	33% helix, 29% strand	Q9WYN2
D	Thymidine kinase (EC 2.7.1.21)	protein	151	33% helix, 26% strand	Q9WYN2

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 4 copies · chains A, D, B, C

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

Pockets

6 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	1139	0.83	0.84	114	empty
2	77	0.37	0.77	17	SO4
3	78	0.36	0.76	19	SO4
4	62	0.34	0.77	17	empty
5	68	0.33	0.76	17	SO4

Interfaces

4 interfaces between chains.

B–D · 1129 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 1102 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 924 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 909 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

2QPO · Thermotoga Maritima Thymidine Kinase in the apo form · the same entry in another collection · chain D against D, TM-score 1.00
Q9WYN2 · AlphaFold monomer V2.0 prediction for thymidine kinase (Q9WYN2) · a predicted model of the same protein · chain C 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 Q9WYN2
Elsewhere: RCSB PDB 2QPO · PDBe 2QPO · UniProt Q9WYN2

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