Structure of PDB 2vnp Chain A

Receptor sequence

>2vnpA (length=176) Species: 511693 (Escherichia coli BL21)

EHVILLNAQGVPTGTLEKYAAHTADTRLHLAFSSWLFNAKGQLLVTRRAL
SKKAWPGVWTNSVCGHPQLGESNEDAVIRRCRYELGVEITPPESIYPDFR
YRATDPSGIVENEVCPVFAARTTSALQINDDEVMDYQWCDLADVLHGIDA
TPWAFSPWMVMQATNREARKRLSAFT

3D structure

• PDB: 2vnp Monoclinic Form of Isopentenyl Diphosphate Isomerase: A Case of Polymorphism in Biomolecular Crystals.
• Chain: A
• Resolution: 2.19 Å

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.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	MN	A	H25 H32 H69 E114 E116	H22 H29 H66 E111 E113
BS02	MG	A	C67 E87	C64 E84
BS03	DED	A	K21 R51 C67 G68 H69 R83 E114 E116 W161	K18 R48 C64 G65 H66 R80 E111 E113 W158	MOAD: Ki=0.12nM PDBbind-CN: -logKd/Ki=9.92,Ki=0.12nM

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)