Structure of PDB 3ivd Chain B

Receptor sequence

>3ivdB (length=499) Species: 217992 (Escherichia coli O6)

AKDVTIIYTNDLHAHVEPYKVPWIADGKRDIGGWANITTLVKQEKAKNKA
TWFFDAGDYFTGPYISSLTKGKAIIDIMNTMPFDAVTIGNHEFDHGWDNT
LLQLSQAKFPIVQGNIFYQNSSKSFWDKPYTIIEKDGVKIGVIGLHGVFA
FNDTVSAATRVGIEARDEIKWLQRYIDELKGKVDLTVALIHEGVPARQSS
MGGTDVRRALDKDIQTASQVKGLDILITGHAHVGTPEPIKVGNTLILSTD
SGGIDVGKLVLDYKEKPHNFTVKNFELKTIYADEWKPDQQTKQVIDGWNK
KLDEVVQQTVAQSPVELKRAYGESASLGNLAADALLAAAGKNTQLALTNS
GGIRNEIPAGAITMGGVISTFPFPNELVTMELTGKQLRSLMEHGASLSNG
VLQVSKGLEMKYDSSKPVGQRVITLTLNGKPIEDATVYHIATQSFLADGG
DGFTAFTEGKARNITGGYYVYHAVVDYFKAGNTITDEQLNGMRVKDIKE

3D structure

• PDB: 3ivd Putative 5'-Nucleotidase (c4898) from Escherichia Coli in complex with Uridine
• Chain: B
• Resolution: 1.9 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D32 H34 D79 N111 H112 D115 H212 H251 H253 Y342 R375
• Catalytic site (residue number reindexed from 1): D11 H13 D58 N90 H91 D94 H191 H230 H232 Y321 R354

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	FE	B	D79 N111 H212 H251	D58 N90 H191 H230
BS02	MN	B	D32 H34 D79 H253	D11 H13 D58 H232
BS03	URI	B	H112 T175 N370 G372 R375 F394 N396 F466 D472	H91 T154 N349 G351 R354 F373 N375 F445 D451

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0016787 hydrolase activity
• GO:0016788 hydrolase activity, acting on ester bonds
• GO:0046872 metal ion binding

Biological Process

• GO:0009166 nucleotide catabolic process

External links

• PDB: RCSB:3ivd, PDBe:3ivd, PDBj:3ivd
• PDBsum: 3ivd
• UniProt: A0A0H2VD83