Structure of PDB 1nfz Chain A

Receptor sequence

>1nfzA (length=176) Species: 562 (Escherichia coli)

EHVILLNAQGVPTGTLEKYAAHTADTRLHLAFSSWLFNAKGQLLVTRRAL
SKKAWPGVWTNSVCGHPQLGESNEDAVIRRCRYELGVEITPPESIYPDFR
YRATDPSGIVENEVCPVFAARTTSALQINDDEVMDYQWCDLADVLHGIDA
TPWAFSPWMVMQATNREARKRLSAFT

3D structure

• PDB: 1nfz Catalytic Mechanism of Escherichia coli Isopentenyl Diphosphate Isomerase Involves Cys-67, Glu-116, and Tyr-104 as Suggested by Crystal Structures of Complexes with Transition State Analogues and Irreversible Inhibitors
• Chain: A
• Resolution: 1.97 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	EIP	A	K21 R51 K55 C67 G68 H69 R83 Y104 E114 E116	K18 R48 K52 C64 G65 H66 R80 Y101 E111 E113

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:1nfz, PDBe:1nfz, PDBj:1nfz
• PDBsum: 1nfz
• PubMed: 12540835
• UniProt: Q46822|IDI_ECOLI Isopentenyl-diphosphate Delta-isomerase (Gene Name=idi)