Structure of PDB 3dh7 Chain D Binding Site BS02

Receptor Information

>3dh7 Chain D (length=313) Species: 300852 (Thermus thermophilus HB8)

KHLEACLEGEVAYQKTTTGLEGFRLRYQALAGLALSEVDLTTPFLGKTLK
APFLIGAMTERINLALAEAAEALGVGMMLGSGRILLERPEAVRKVAPKAL
LIANLGLAQLRRYGRDDLLRLVEMLEADALAFHVNPLQEAVQRGDTDFRG
LVERLAELLPLPFPVMVKEVGHGLSREAALALRDLPLAAVDVAGAGGTSW
ARVEEWVRFGEVRHPELCEIGIPTARAILEVREVLPHLPLVASGGVYTGT
DGAKALALGADLLAVARPLLRPALEGAERVAAWIGDYLEELRTALFAIGA
RNPKEARGRVERV

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: 3dh7 Chain D Residue 503

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3dh7 Crystal structure of type 2 isopentenyl diphosphate isomerase from Thermus thermophilus in complex with inorganic pyrophosphate
• Resolution: 2.97 Å
• Binding residue (original residue number in PDB): S95 R97 L124 G125 Q128 H152
• Binding residue (residue number reindexed from 1): S81 R83 L105 G106 Q109 H133
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 5.3.3.2: isopentenyl-diphosphate Delta-isomerase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0000287 magnesium ion binding
• GO:0004452 isopentenyl-diphosphate delta-isomerase activity
• GO:0010181 FMN binding
• GO:0016491 oxidoreductase activity
• GO:0016853 isomerase activity
• GO:0046872 metal ion binding
• GO:0070402 NADPH binding

Biological Process

• GO:0008299 isoprenoid biosynthetic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:3dh7, PDBe:3dh7, PDBj:3dh7
• PDBsum: 3dh7
• PubMed: 18693754
• UniProt: Q53W52