Structure of PDB 5nh9 Chain D Binding Site BS05

Receptor Information
>5nh9 Chain D (length=436) Species: 73868 (Piromyces sp. E2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AKEYFPQIQKIKFEGKDSKNPLAFHYYDAEKEVMGKKMKDWLRFAMAWWH
TLCAEGADQFGGGTKSFPWNEGTDAIEIAKQKVDAGFEIMQKLGIPYYCF
HDVDLVSEGNSIEEYESNLKAVVAYLKEKQKETGIKLLWSTANVFGHKRY
MNGASTNPDFDVVARAIVQIKNAIDAGIELGAENYVFWGGREGYMSLLNT
DQKREKEHMATMLTMARDYARSKGFKGTFLIEPKPMEPTKHQYDVDTETA
IGFLKAHNLDKDFKVNIEVNHATLAGHTFEHELACAVDAGMLGSIDANRG
DYQNGWDTDQFPIDQYELVQAWMEIIRGGGFVTGGTNFDAKTRRNSTDLE
DIIIAHVSGMDAMARALENAAKLLQESPYTKMKKERYASFDSGIGKDFED
GKLTLEQVYEYGKKNGEPKQTSGKQELYEAIVAMYQ
Ligand information
Ligand IDXLS
InChIInChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h1,3-5,7-10H,2H2/t3-,4+,5+/m0/s1
InChIKeyPYMYPHUHKUWMLA-VPENINKCSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=CC(O)C(O)C(O)CO
CACTVS 3.341OC[CH](O)[CH](O)[CH](O)C=O
OpenEye OEToolkits 1.5.0C([C@H]([C@@H]([C@H](C=O)O)O)O)O
CACTVS 3.341OC[C@@H](O)[C@H](O)[C@@H](O)C=O
OpenEye OEToolkits 1.5.0C(C(C(C(C=O)O)O)O)O
FormulaC5 H10 O5
NameD-xylose;
D-XYLOSE (LINEAR FORM)
ChEMBLCHEMBL1236821
DrugBankDB09419
ZINCZINC000018168715
PDB chain5nh9 Chain D Residue 504 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5nh9 Metal Dependence of the Xylose Isomerase from Piromyces sp. E2 Explored by Activity Profiling and Protein Crystallography.
Resolution2.08 Å
Binding residue
(original residue number in PDB)		H102 W189 E233 E269 H272 D340
Binding residue
(residue number reindexed from 1)		H101 W188 E232 E268 H271 D339
Annotation score1
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) H101 D104 W139 E232 K234 E268 H271 D296 D307 D309 D339
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5nh9, PDBe:5nh9, PDBj:5nh9
PDBsum5nh9
PubMed29045784
UniProtQ9P8C9

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