Structure of PDB 3t80 Chain D Binding Site BS03

Receptor Information

>3t80 Chain D (length=157) Species: 90371 (Salmonella enterica subsp. enterica serovar Typhimurium)

AMRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALL
GAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTII
AQAPKMLPHIPQMRVFIAEDLGCHMDEVNVKATTTEKLGFTGRGEGIACE
AVALLMK

Ligand information

• Ligand ID: POP
• InChI: InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)/p-2
• InChIKey: XPPKVPWEQAFLFU-UHFFFAOYSA-L
• SMILES:
  OpenEye OEToolkits 1.5.0: O[P@@](=O)([O-])O[P@@](=O)(O)[O-]
  CACTVS 3.341: O[P]([O-])(=O)O[P](O)([O-])=O
  ACDLabs 10.04: [O-]P(=O)(O)OP([O-])(=O)O
  OpenEye OEToolkits 1.5.0: OP(=O)([O-])OP(=O)(O)[O-]
• Formula: H2 O7 P2
• Name: PYROPHOSPHATE 2-
• PDB chain: 3t80 Chain E Residue 160

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3t80 Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella typhimurium bound to cytidine
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): G138 F139 R142
• Binding residue (residue number reindexed from 1): G139 F140 R143
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 4.6.1.12: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase.

Gene Ontology

Molecular Function

• GO:0008685 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
• GO:0016829 lyase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0008299 isoprenoid biosynthetic process
• GO:0016114 terpenoid biosynthetic process
• GO:0019288 isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway

External links

• PDB: RCSB:3t80, PDBe:3t80, PDBj:3t80
• PDBsum: 3t80
• UniProt: Q8ZMF7|ISPF_SALTY 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (Gene Name=ispF)