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Crystal structure of R145E mutant of thymidylate kinase (AQ_969) from aquifex aeolicus VF5

Analyse Crystal structure of R145E mutant of thymidylate kinase (AQ_969) from aquifex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5XBH
Type: protein
Length: 388 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thymidylate kinase
EC: 2.7.4.9
UniProt: O67099
Pockets: 5 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 58% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Thymidylate kinase (EC 2.7.4.9)	protein	194	58% helix, 13% strand	O67099

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	367	0.61	0.77	40	empty
2	227	0.61	0.81	25	empty
3	107	0.52	0.82	16	empty
4	110	0.51	0.81	19	empty
5	88	0.38	0.76	19	empty

Interfaces

1 interface between chains.

A–B · 1116 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

5XBH · Crystal structure of R145E mutant of thymidylate kinase (aq_969) from Aquifex Aeolicus VF5 · the same entry in another collection · chain A against A, TM-score 1.00
O67099 · AlphaFold monomer V2.0 prediction for thymidylate kinase (O67099) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 O67099
Elsewhere: RCSB PDB 5XBH · PDBe 5XBH · UniProt O67099

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