Structure of PDB 5nh9 Chain D

Receptor sequence

>5nh9D (length=436) Species: 73868 (Piromyces sp. E2)

AKEYFPQIQKIKFEGKDSKNPLAFHYYDAEKEVMGKKMKDWLRFAMAWWH
TLCAEGADQFGGGTKSFPWNEGTDAIEIAKQKVDAGFEIMQKLGIPYYCF
HDVDLVSEGNSIEEYESNLKAVVAYLKEKQKETGIKLLWSTANVFGHKRY
MNGASTNPDFDVVARAIVQIKNAIDAGIELGAENYVFWGGREGYMSLLNT
DQKREKEHMATMLTMARDYARSKGFKGTFLIEPKPMEPTKHQYDVDTETA
IGFLKAHNLDKDFKVNIEVNHATLAGHTFEHELACAVDAGMLGSIDANRG
DYQNGWDTDQFPIDQYELVQAWMEIIRGGGFVTGGTNFDAKTRRNSTDLE
DIIIAHVSGMDAMARALENAAKLLQESPYTKMKKERYASFDSGIGKDFED
GKLTLEQVYEYGKKNGEPKQTSGKQELYEAIVAMYQ

3D structure

• PDB: 5nh9 Metal Dependence of the Xylose Isomerase from Piromyces sp. E2 Explored by Activity Profiling and Protein Crystallography.
• Chain: D
• Resolution: 2.08 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): H101 D104 W139 E232 K234 E268 H271 D296 D307 D309 D339
• 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	XYP	D	K204 H258	K203 H257
BS02	XYP	D	D289 A290	D288 A289
BS03	MN	D	E233 E269 D297 D340	E232 E268 D296 D339
BS04	MN	D	E269 H272 D308 D310	E268 H271 D307 D309
BS05	XLS	D	H102 W189 E233 E269 H272 D340	H101 W188 E232 E268 H271 D339
BS06	XYP	D	K40 D41 Y98 K137	K39 D40 Y97 K136

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:5nh9, PDBe:5nh9, PDBj:5nh9
• PDBsum: 5nh9
• PubMed: 29045784
• UniProt: Q9P8C9