MolNFT v1 · #139271 · protein

Y99F mutant of thermus thermophilus HB8 thymidylate kinase

5XAL: “Y99F mutant of thermus thermophilus HB8 thymidylate kinase”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.57). MolNFT v1 #139271 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XAL
Type: protein
Length: 366 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: MG
Pockets: 4 · best druggability 0.57

Structure

x-ray diffraction · 2 distinct chains · 54% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thymidylate kinase (EC 2.7.4.9)	protein	185	56% helix, 15% strand	Q5SHX3
B	Thymidylate kinase (EC 2.7.4.9)	protein	181	52% helix, 15% strand	Q5SHX3

Ligands and binding sites

MG · Magnesium ion · metal · 8 copies · chains A, B
FMT · Formic acid · additive · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	271	0.57	0.77	34	FMT
2	79	0.44	0.81	15	empty
3	131	0.42	0.76	24	empty
4	75	0.40	0.79	14	empty

Interfaces

1 interface between chains.

A–B · 1086 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

5XAL · Y99F mutant of Thermus thermophilus HB8 thymidylate kinase · the same entry in another collection · chain A against A, 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 5XAL · PDBe 5XAL · UniProt Q5SHX3

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