Structure of PDB 5olc Chain D Binding Site BS01

Receptor Information

>5olc Chain D (length=351) Species: 63186 (Zobellia galactanivorans)

SKIKKIEPYVISHKLDDTRKICIVKITLDDGTYGWGEGYGPAAVIKSGID
FFTPFLLGKEAIGHEVLWQEMYRRSMDYARSGVLQAAISAIDVALWDIKG
KLLNLPVSVLLGGVKNPIIEPYATGLYLEELLVEEALLYKSQGFKATKMK
VGLGIEQDLKYIAAIRKAIGPDMRLMIDSNHAYCYKEAIELARKAEKFDI
SWFEEPVSPEDYDGYKRLRQNTTIPISGGECEYLKYGFKRLFDKDCVDIA
QPDICAAGGLTEVKKIATLAQTYNVDLVPHTWGTWIAISAAVHLVANLDL
PTMELDRTENALRDEVTLHKIKLENGHLEVPCTPGLGVDVDMDKLEHYLD
K

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 5olc Chain D Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5olc Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic bacteria.
• Resolution: 2.79 Å
• Binding residue (original residue number in PDB): D194 E220 E246 H296
• Binding residue (residue number reindexed from 1): D178 E204 E230 H280
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): K164 K166 D194 N196 E220 G245 E246 D269 H296 E329 E334
• Catalytic site (residue number reindexed from 1): K148 K150 D178 N180 E204 G229 E230 D253 H280 E304 E309
• Enzyme Commision number: 4.2.1.6: galactonate dehydratase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0008869 galactonate dehydratase activity
• GO:0016829 lyase activity
• GO:0016836 hydro-lyase activity
• GO:0016853 isomerase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0009063 amino acid catabolic process
• GO:0016052 carbohydrate catabolic process

External links

• PDB: RCSB:5olc, PDBe:5olc, PDBj:5olc
• PDBsum: 5olc
• PubMed: 29162826
• UniProt: G0L7B8