Structure of PDB 2dho Chain A Binding Site BS06

Receptor Information

>2dho Chain A (length=215) Species: 9606 (Homo sapiens)

QVQLLAEMCILIDENDNKIGAETKKNCHLNENIEKGLLHRAFSVFLFNTE
NKLLLQQRSDAKITFPGCFTNTCCSHPLSNPAELEESDALGVRRAAQRRL
KAELGIPLEEVPPEEINYLTRIHYKAQSDGIWGEHEIDYILLVRMNVTLN
PDPNEIKSYCYVSKEELKELLKKAASGEIKITPWFKIIAATFLFKWWDNL
NHLNQFVDHEKIYRM

Ligand information

• Ligand ID: MN
• InChI: InChI=1S/Mn/q+2
• InChIKey: WAEMQWOKJMHJLA-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mn+2]
  CACTVS 3.341: [Mn++]
• Formula: Mn
• Name: MANGANESE (II) ION
• DrugBank: DB06757
• PDB chain: 2dho Chain A Residue 1008

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2dho Crystal structures of human IPP isomerase: new insights into the catalytic mechanism
• Resolution: 1.6 Å
• Binding residue (original residue number in PDB): E97 S99
• Binding residue (residue number reindexed from 1): E85 S87
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H51 C86 H88 E115 Y136 E146 E148 W196
• Catalytic site (residue number reindexed from 1): H39 C74 H76 E103 Y124 E134 E136 W184
• Enzyme Commision number: 5.3.3.2: isopentenyl-diphosphate Delta-isomerase.

Gene Ontology

Molecular Function

• GO:0004452 isopentenyl-diphosphate delta-isomerase activity
• GO:0016853 isomerase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006695 cholesterol biosynthetic process
• GO:0008299 isoprenoid biosynthetic process
• GO:0009240 isopentenyl diphosphate biosynthetic process
• GO:0050992 dimethylallyl diphosphate biosynthetic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0005777 peroxisome
• GO:0005829 cytosol

External links

• PDB: RCSB:2dho, PDBe:2dho, PDBj:2dho
• PDBsum: 2dho
• PubMed: 17137593
• UniProt: Q13907|IDI1_HUMAN Isopentenyl-diphosphate Delta-isomerase 1 (Gene Name=IDI1)