Structure of PDB 2vnp Chain B Binding Site BS01

Receptor Information

>2vnp Chain B (length=180) Species: 511693 (Escherichia coli BL21)

EHVILLNAQGVPTGTLEKYAAHTADTRLHLAFSSWLFNAKGQLLVTRRAL
SKKAWPGVWTNSVCGHPQLGESNEDAVIRRCRYELGVEITPPESIYPDFR
YRATDPSGIVENEVCPVFAARTTSALQINDDEVMDYQWCDLADVLHGIDA
TPWAFSPWMVMQATNREARKRLSAFTQLKL

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: 2vnp Chain B Residue 1184

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2vnp Monoclinic Form of Isopentenyl Diphosphate Isomerase: A Case of Polymorphism in Biomolecular Crystals.
• Resolution: 2.19 Å
• Binding residue (original residue number in PDB): H25 H32 H69 E114 E116
• Binding residue (residue number reindexed from 1): H22 H29 H66 E111 E113
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H25 H32 C67 H69 E87 Y104 E114 E116 W161
• Catalytic site (residue number reindexed from 1): H22 H29 C64 H66 E84 Y101 E111 E113 W158
• Enzyme Commision number: 5.3.3.2: isopentenyl-diphosphate Delta-isomerase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003824 catalytic activity
• GO:0004452 isopentenyl-diphosphate delta-isomerase activity
• GO:0008270 zinc ion binding
• GO:0016853 isomerase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006974 DNA damage response
• GO:0008299 isoprenoid biosynthetic process
• GO:0050992 dimethylallyl diphosphate biosynthetic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:2vnp, PDBe:2vnp, PDBj:2vnp
• PDBsum: 2vnp
• PubMed: 18391416
• UniProt: Q46822|IDI_ECOLI Isopentenyl-diphosphate Delta-isomerase (Gene Name=idi)