Structure of PDB 5yn3 Chain B

Receptor sequence

>5yn3B (length=435) Species: 73868 (Piromyces sp. E2)

KEYFPQIQKIKFEGKDSKNPLAFHYYDAEKEVMGKKMKDWLRFAMAWWHT
LCAEGADQFGGGTKSFPWNEGTDAIEIAKQKVDAGFEIMQKLGIPYYCFH
DVDLVSEGNSIEEYESNLKAVVAYLKEKQKETGIKLLWSTANVFGHKRYM
NGASTNPDFDVVARAIVQIKNAIDAGIELGAENYVFWGGREGYMSLLNTD
QKREKEHMATMLTMARDYARSKGFKGTFLIEPKPMEPTKHQYDVDTETAI
GFLKAHNLDKDFKVNIEVNHATLAGHTFEHELACAVDAGMLGSIDANRGD
YQNGWDTDQFPIDQYELVQAWMEIIRGGGFVTGGTNFDAKTRRNSTDLED
IIIAHVSGMDAMARALENAAKLLQESPYTKMKKERYASFDSGIGKDFEDG
KLTLEQVYEYGKKNGEPKQTSGKQELYEAIVAMYQ

3D structure

• PDB: 5yn3 Crystal Structure and Biochemical Characterization of Xylose Isomerase fromPiromycessp. E2.
• Chain: B
• Resolution: 2.7 Å

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.

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	MN	B	E269 H272 D308 D310	E267 H270 D306 D308
BS02	MN	B	E233 E269 D297 D340	E231 E267 D295 D338
BS03	GOL	B	W50 H102 W189 E233 D297 D340	W48 H100 W187 E231 D295 D338

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