Structure of PDB 8u0m Chain B Binding Site BS02

Receptor Information

>8u0m Chain B (length=247) Species: 582419 (Thermococcus paralvinellae)

SHMIIIKLGGSVISDSFHRHIVEQIAEEIAQFYPDESFILVHGGGSFGHP
NAREYKITEGLVGDVDRKRIGFSKTHQAMLKLNDLIIQTFLEKGLPAYSV
SSSSIFLLENKEVVYGELEILRKLLELKFIPVLFGDTAIALDKGIDILSG
DQIVSYLAKMLKPSKVIFLMDVDGIYDRNPKERDAKLIEELNVEEIRHLL
ESIGNKLREALKIAKHSEVYFINGKVKENLGKAIRGEKVGTRLRKLE

Ligand information

• Ligand ID: U5O
• InChI: InChI=1S/C5H11O4P/c1-3-5(2)4-9-10(6,7)8/h3H,4H2,1-2H3,(H2,6,7,8)/b5-3+
• InChIKey: LEHUQIAIMZSVST-HWKANZROSA-N
• SMILES:
  ACDLabs 12.01: O=P(O)(O)OCC(\C)=C\C
  CACTVS 3.385: C/C=C(C)/CO[P](O)(O)=O
  OpenEye OEToolkits 2.0.7: CC=C(C)COP(=O)(O)O
  OpenEye OEToolkits 2.0.7: C/C=C(\C)/COP(=O)(O)O
  CACTVS 3.385: CC=C(C)CO[P](O)(O)=O
• Formula: C5 H11 O4 P
• Name: (2E)-2-methylbut-2-en-1-yl dihydrogen phosphate
• PDB chain: 8u0m Chain B Residue 302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8u0m Ternary complexes of isopentenyl phosphate kinase from Thermococcus paralvinellae reveal molecular determinants of non-natural substrate specificity.
• Resolution: 2.54 Å
• Binding residue (original residue number in PDB): G51 H52 G138
• Binding residue (residue number reindexed from 1): G48 H49 G135
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.7.4.26: isopentenyl phosphate kinase.

Gene Ontology

Molecular Function

• GO:0005524 ATP binding
• GO:0016301 kinase activity
• GO:0102043 isopentenyl phosphate kinase activity

Biological Process

• GO:0008299 isoprenoid biosynthetic process
• GO:0016310 phosphorylation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:8u0m, PDBe:8u0m, PDBj:8u0m
• PDBsum: 8u0m
• PubMed: 38333996
• UniProt: W0I5G2