Structure of PDB 5nh8 Chain D Binding Site BS02

Receptor Information

>5nh8 Chain D (length=436) Species: 73868 (Piromyces sp. E2)

AKEYFPQIQKIKFEGKDSKNPLAFHYYDAEKEVMGKKMKDWLRFAMAWWH
TLCAEGADQFGGGTKSFPWNEGTDAIEIAKQKVDAGFEIMQKLGIPYYCF
HDVDLVSEGNSIEEYESNLKAVVAYLKEKQKETGIKLLWSTANVFGHKRY
MNGASTNPDFDVVARAIVQIKNAIDAGIELGAENYVFWGGREGYMSLLNT
DQKREKEHMATMLTMARDYARSKGFKGTFLIEPKPMEPTKHQYDVDTETA
IGFLKAHNLDKDFKVNIEVNHATLAGHTFEHELACAVDAGMLGSIDANRG
DYQNGWDTDQFPIDQYELVQAWMEIIRGGGFVTGGTNFDAKTRRNSTDLE
DIIIAHVSGMDAMARALENAAKLLQESPYTKMKKERYASFDSGIGKDFED
GKLTLEQVYEYGKKNGEPKQTSGKQELYEAIVAMYQ

Ligand information

• Ligand ID: CA
• InChI: InChI=1S/Ca/q+2
• InChIKey: BHPQYMZQTOCNFJ-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Ca++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Ca+2]
• Formula: Ca
• Name: CALCIUM ION
• DrugBank: DB14577
• PDB chain: 5nh8 Chain D Residue 502

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5nh8 Metal Dependence of the Xylose Isomerase from Piromyces sp. E2 Explored by Activity Profiling and Protein Crystallography.
• Resolution: 1.86 Å
• Binding residue (original residue number in PDB): E269 H272 D308 D310
• Binding residue (residue number reindexed from 1): E268 H271 D307 D309
• 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): 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

External links

• PDB: RCSB:5nh8, PDBe:5nh8, PDBj:5nh8
• PDBsum: 5nh8
• PubMed: 29045784
• UniProt: Q9P8C9