Structure of PDB 5yn3 Chain B Binding Site BS03

Receptor Information

>5yn3 Chain B (length=435) Species: 73868 (Piromyces sp. E2)

KEYFPQIQKIKFEGKDSKNPLAFHYYDAEKEVMGKKMKDWLRFAMAWWHT
LCAEGADQFGGGTKSFPWNEGTDAIEIAKQKVDAGFEIMQKLGIPYYCFH
DVDLVSEGNSIEEYESNLKAVVAYLKEKQKETGIKLLWSTANVFGHKRYM
NGASTNPDFDVVARAIVQIKNAIDAGIELGAENYVFWGGREGYMSLLNTD
QKREKEHMATMLTMARDYARSKGFKGTFLIEPKPMEPTKHQYDVDTETAI
GFLKAHNLDKDFKVNIEVNHATLAGHTFEHELACAVDAGMLGSIDANRGD
YQNGWDTDQFPIDQYELVQAWMEIIRGGGFVTGGTNFDAKTRRNSTDLED
IIIAHVSGMDAMARALENAAKLLQESPYTKMKKERYASFDSGIGKDFEDG
KLTLEQVYEYGKKNGEPKQTSGKQELYEAIVAMYQ

Ligand information

• Ligand ID: GOL
• InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
• InChIKey: PEDCQBHIVMGVHV-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: C(C(CO)O)O
  ACDLabs 12.01
  CACTVS 3.370: OCC(O)CO
• Formula: C3 H8 O3
• Name: GLYCEROL;
  GLYCERIN;
  PROPANE-1,2,3-TRIOL
• ChEMBL: CHEMBL692
• DrugBank: DB09462
• ZINC: ZINC000000895048
• PDB chain: 5yn3 Chain B Residue 503

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5yn3 Crystal Structure and Biochemical Characterization of Xylose Isomerase fromPiromycessp. E2.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): W50 H102 W189 E233 D297 D340
• Binding residue (residue number reindexed from 1): W48 H100 W187 E231 D295 D338
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H102 D105 W140 E233 K235 E269 H272 D297 D308 D310 D340
• Catalytic site (residue number reindexed from 1): H100 D103 W138 E231 K233 E267 H270 D295 D306 D308 D338
• Enzyme Commision number: 5.3.1.5: xylose isomerase.

Gene Ontology

Molecular Function

• GO:0009045 xylose isomerase activity
• GO:0016853 isomerase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0005975 carbohydrate metabolic process
• GO:0042732 D-xylose metabolic process
• GO:0044577 D-xylose catabolic process to ethanol

External links

• PDB: RCSB:5yn3, PDBe:5yn3, PDBj:5yn3
• PDBsum: 5yn3
• PubMed: 29385668
• UniProt: Q9P8C9