Structure of PDB 3ivd Chain A

Receptor sequence

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

LAKDVTIIYTNDLHAHVEPYKVPWIADGKRDIGGWANITTLVKQEKAKNK
ATWFFDAGDYFTGPYISSLTKGKAIIDIMNTMPFDAVTIGNHEFDHGWDN
TLLQLSQAKFPIVQGNIFYQNSSKSFWDKPYTIIEKDGVKIGVIGLHGVF
AFNDTVSAATRVGIEARDEIKWLQRYIDELKGKVDLTVALIHEGVPARQS
SMGGTDVRRALDKDIQTASQVKGLDILITGHAHVGTPEPIKVGNTLILST
DSGGIDVGKLVLDYKEKPHNFTVKNFELKTIYADEWKPDQQTKQVIDGWN
KKLDEVVQQTVAQSPVELKRAYGESASLGNLAADALLAAAGKNTQLALTN
SGGIRNEIPAGAITMGGVISTFPFPNELVTMELTGKQLRSLMEHGASLSN
GVLQVSKGLEMKYDSSKPVGQRVITLTLNGKPIEDATVYHIATQSFLADG
GDGFTAFTEGKARNITGGYYVYHAVVDYFKAGNTITDEQLNGMRVKDIK

3D structure

• PDB: 3ivd Putative 5'-Nucleotidase (c4898) from Escherichia Coli in complex with Uridine
• Chain: A
• 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): D12 H14 D59 N91 H92 D95 H192 H231 H233 Y322 R355

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	A	D79 N111 H212 H251	D59 N91 H192 H231
BS02	MN	A	D32 H34 D79 H253	D12 H14 D59 H233
BS03	URI	A	H112 T175 N370 G372 R375 F394 N396 F466 D472	H92 T155 N350 G352 R355 F374 N376 F446 D452

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