MolNFT v1 · #139203 · protein

D90L mutant of thermus thermophilus HB8 thymidylate kinase

5X8D: “D90L mutant of thermus thermophilus HB8 thymidylate kinase”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.49). MolNFT v1 #139203 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5X8D
Type: protein
Length: 369 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 0.49

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Thymidylate kinase (EC 2.7.4.9)	protein	184	55% helix, 15% strand	Q5SHX3
A	Thymidylate kinase (EC 2.7.4.9)	protein	185	53% helix, 15% strand	Q5SHX3

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains B, A
PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains B, A

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

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	165	0.49	0.77	23	empty
2	156	0.48	0.77	28	PEG
3	62	0.39	0.80	13	empty
4	62	0.38	0.80	14	empty

Interfaces

1 interface between chains.

B–A · 1085 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

5X8D · D90L mutant of thermus thermophilus HB8 thymidylate kinase · 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 B 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 5X8D · PDBe 5X8D · UniProt Q5SHX3

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