Structure of PDB 5zb4 Chain B Binding Site BS02

Receptor Information

>5zb4 Chain B (length=185) Species: 300852 (Thermus thermophilus HB8)

GLFLTLEGLDGSGKTTQARRLAAFLEAQGRPVLLTREPGGGLPEVRSLLL
TQELSPEAEYLLFSADRAEHVRKVILPGLAAGKVVISDRYLDSSLAYQGY
GRGLPLPWLREVAREATRGLKPRLTFLLDLPPEAALLGLEFFRRVREGYL
ALARAEPGRFVVLDATLPEEEIARAIQAHLRPLLP

Ligand information

• Ligand ID: CA
• InChI: InChI=1S/Ca/q+2
• InChIKey: BHPQYMZQTOCNFJ-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Ca++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Ca+2]
• Formula: Ca
• Name: CALCIUM ION
• DrugBank: DB14577
• PDB chain: 5zb4 Chain B Residue 203

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5zb4 Insights into product release dynamics through structural analyses of thymidylate kinase.
• Resolution: 1.92 Å
• Binding residue (original residue number in PDB): Y62 S66 R69 A115
• Binding residue (residue number reindexed from 1): Y60 S64 R67 A113
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.7.4.9: dTMP kinase.

Gene Ontology

Molecular Function

• GO:0004798 thymidylate kinase activity
• GO:0005524 ATP binding
• GO:0016301 kinase activity

Biological Process

• GO:0006227 dUDP biosynthetic process
• GO:0006233 dTDP biosynthetic process
• GO:0006235 dTTP biosynthetic process
• GO:0009165 nucleotide biosynthetic process
• GO:0016310 phosphorylation
• GO:0046940 nucleoside monophosphate phosphorylation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:5zb4, PDBe:5zb4, PDBj:5zb4
• PDBsum: 5zb4
• PubMed: 30447376
• UniProt: Q5SHX3|KTHY_THET8 Thymidylate kinase (Gene Name=tmk)