Structure of PDB 3jyf Chain B Binding Site BS01

Receptor Information

>3jyf Chain B (length=335) Species: 272620 (Klebsiella pneumoniae subsp. pneumoniae MGH 78578)

AATVDLRIMETTDLHSNMMDFDYYKDAATEKFGLVRTASLIEQARAEVKN
SVLVDNGDVIQGSPLGDYMAAKGLKEGDVHPVYKAMNTLNYAVGNLGNHE
FNYGLDFLHKALAGAKFPYVNANIIDAKTGKPMFTPYLIQDTRVVDSDGQ
IHTLRIGYIGFVPPQIMTWDKANLNGKVTVNDITETARKYIPEMRAKGAD
VVVVVAHSGLSADPYQAMAENSVYYLSQVPGVDAIMFGHAHAVFPGKDFA
NIKGADIAKGTLNGVPAVMPGMWGDHLGVVDLVLNNDSGKWQVTQSKAEA
RPIYDAVAKKSLAAEDGKLVSVLKADHDATREFVS

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: 3jyf Chain B Residue 340

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3jyf The crystal structure of a 2,3-cyclic nucleotide 2-phosphodiesterase/3-nucleotidase bifunctional periplasmic precursor protein from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
• Resolution: 2.43 Å
• Binding residue (original residue number in PDB): D61 N101 H210 H242
• Binding residue (residue number reindexed from 1): D58 N98 H207 H239
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D16 H18 D61 N101 H102 N105 H210 H242 H244
• Catalytic site (residue number reindexed from 1): D13 H15 D58 N98 H99 N102 H207 H239 H241
• Enzyme Commision number: 3.1.3.6: 3'-nucleotidase.
  3.1.4.16: 2',3'-cyclic-nucleotide 2'-phosphodiesterase.

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:3jyf, PDBe:3jyf, PDBj:3jyf
• PDBsum: 3jyf
• UniProt: A6THC4