Structure of PDB 3ivd Chain B Binding Site BS02

Receptor Information

>3ivd Chain B (length=499) Species: 217992 (Escherichia coli O6)

AKDVTIIYTNDLHAHVEPYKVPWIADGKRDIGGWANITTLVKQEKAKNKA
TWFFDAGDYFTGPYISSLTKGKAIIDIMNTMPFDAVTIGNHEFDHGWDNT
LLQLSQAKFPIVQGNIFYQNSSKSFWDKPYTIIEKDGVKIGVIGLHGVFA
FNDTVSAATRVGIEARDEIKWLQRYIDELKGKVDLTVALIHEGVPARQSS
MGGTDVRRALDKDIQTASQVKGLDILITGHAHVGTPEPIKVGNTLILSTD
SGGIDVGKLVLDYKEKPHNFTVKNFELKTIYADEWKPDQQTKQVIDGWNK
KLDEVVQQTVAQSPVELKRAYGESASLGNLAADALLAAAGKNTQLALTNS
GGIRNEIPAGAITMGGVISTFPFPNELVTMELTGKQLRSLMEHGASLSNG
VLQVSKGLEMKYDSSKPVGQRVITLTLNGKPIEDATVYHIATQSFLADGG
DGFTAFTEGKARNITGGYYVYHAVVDYFKAGNTITDEQLNGMRVKDIKE

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: 3ivd Chain B Residue 602

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3ivd Putative 5'-Nucleotidase (c4898) from Escherichia Coli in complex with Uridine
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): D32 H34 D79 H253
• Binding residue (residue number reindexed from 1): D11 H13 D58 H232
• Annotation score: 4

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

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