Structure of PDB 5y4j Chain A Binding Site BS02

Receptor Information
>5y4j Chain A (length=384) Species: 1929 (Streptomyces rubiginosus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YQPTPEDRFTFGLWTVGWEGRDPFGDATRRALDPVESVRRLAELGAHGVT
FHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDG
GFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVR
DALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAF
IERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGI
KYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWAS
AAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLD
DRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGA
Ligand information
Ligand IDXYL
InChIInChI=1S/C5H12O5/c6-1-3(8)5(10)4(9)2-7/h3-10H,1-2H2/t3-,4+,5+
InChIKeyHEBKCHPVOIAQTA-SCDXWVJYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C([C@@H](C([C@@H](CO)O)O)O)O
OpenEye OEToolkits 1.5.0C(C(C(C(CO)O)O)O)O
CACTVS 3.341OC[CH](O)[CH](O)[CH](O)CO
CACTVS 3.341OC[C@H](O)[C@@H](O)[C@H](O)CO
ACDLabs 10.04OC(CO)C(O)C(O)CO
FormulaC5 H12 O5
NameXylitol;
D-Xylitol
ChEMBLCHEMBL96783
DrugBankDB11195
ZINCZINC000100018612
PDB chain5y4j Chain A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5y4j Crystal structure of glucose isomerase in complex with xylitol inhibitor in one metal binding mode
Resolution1.4 Å
Binding residue
(original residue number in PDB)		H54 W137 E181 K183 E217 H220 D287
Binding residue
(residue number reindexed from 1)		H52 W135 E179 K181 E215 H218 D285
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H54 D57 M88 E181 K183 E217 H220 D245 D255 D257 D287
Catalytic site (residue number reindexed from 1) H52 D55 M86 E179 K181 E215 H218 D243 D253 D255 D285
Enzyme Commision number 5.3.1.5: xylose isomerase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0009045 xylose isomerase activity
GO:0016853 isomerase activity
GO:0042802 identical protein binding
GO:0046872 metal ion binding
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0042732 D-xylose metabolic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5y4j, PDBe:5y4j, PDBj:5y4j
PDBsum5y4j
PubMed28865958
UniProtP24300|XYLA_STRRU Xylose isomerase (Gene Name=xylA)

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