Structure of PDB 6f4x Chain D

Receptor sequence

>6f4xD (length=233) Species: 210 (Helicobacter pylori)

MTPHINAKIGDFYPQCLLCGDPLRVSYIAKKFLQDAKEITNVRNMLGFSG
KYKGRGISLMGHGMGIASCTIYVTELIKTYQVKELLRIGTCGAISPKVGL
KDIIMATGASTDSKTNRVRFLNHDLSATPDFELSLRAYQTAKRLGIDLKV
GNVFSSDFFYSFETHAFDLMAKYNHLAIEMEAAGLYATAMELNAKALCLC
SVSDHLITKEALSPKERVESFDNMIILALEMMS

3D structure

• PDB: 6f4x Helicobacter pylori purine nucleoside phosphorylase shows new distribution patterns of open and closed active site conformations and unusual biochemical features.
• Chain: D
• Resolution: 1.694 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H4 G20 R24 R43 E75 R87 T90 S203 D204 L206 R217
• Catalytic site (residue number reindexed from 1): H4 G20 R24 R43 E75 R87 T90 S203 D204 L206 R217
• Enzyme Commision number: 2.4.2.1: purine-nucleoside phosphorylase.

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	FMC	D	H4 R43	H4 R43	MOAD: Kd=10.7uM PDBbind-CN: -logKd/Ki=4.97,Kd=10.7uM
BS02	FMC	D	M64 T90 C91 G92 F159 E181	M64 T90 C91 G92 F159 E181	MOAD: Kd=10.7uM PDBbind-CN: -logKd/Ki=4.97,Kd=10.7uM

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0004731 purine-nucleoside phosphorylase activity
• GO:0016757 glycosyltransferase activity
• GO:0016763 pentosyltransferase activity

Biological Process

• GO:0006139 nucleobase-containing compound metabolic process
• GO:0006152 purine nucleoside catabolic process
• GO:0009116 nucleoside metabolic process
• GO:0009164 nucleoside catabolic process

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:6f4x, PDBe:6f4x, PDBj:6f4x
• PDBsum: 6f4x
• PubMed: 29430816
• UniProt: P56463|DEOD_HELPY Purine nucleoside phosphorylase DeoD-type (Gene Name=deoD)