Structure of PDB 4xda Chain A

Receptor sequence

>4xdaA (length=306) Species: 345073 (Vibrio cholerae O395)

MNKLVVLGSVNADHVLQVPSFPRPGETLHGRNYQVIPGGKGANQAVAAAR
MQADVGFIACVGDDSFGINIRESFKLDGINTAGVKLQPNCPTGIAMIQVS
DSGENSICISAEANAKLTAAAIEPDLAAIRDARYLLMQLETPLDGILKAA
QEAKTAKTNVILNPAPARELPDELLKCVDLITPNETEAEVLTGITVYDDS
SAQQAADALHCKGIEIVIITLGSKGVWLSQNGRGQRIPGFVVKATDTTAA
GDTFNGALVTGLLQEMPLESAIKFAHAAAAISVTRFGAQTSIPTRAEVEA
FLAEHS

3D structure

• PDB: 4xda Crystal Structure of Apo and Ligand Bound Vibrio cholerae Ribokinase (Vc-RK): Role of Monovalent Cation Induced Activation and Structural Flexibility in Sugar Phosphorylation
• Chain: A
• Resolution: 1.75 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): A249 A250 G251 D252
• Catalytic site (residue number reindexed from 1): A249 A250 G251 D252
• Enzyme Commision number: 2.7.1.15: ribokinase.

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	RIB	A	N11 D13 G39 K40 N43 A95 E140 D252	N11 D13 G39 K40 N43 A95 E140 D252
BS02	ADP	A	N184 G222 S223 V242 H276 A279 V283	N184 G222 S223 V242 H276 A279 V283

Gene Ontology

Molecular Function

• GO:0004747 ribokinase activity
• GO:0005524 ATP binding
• GO:0016301 kinase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006014 D-ribose metabolic process
• GO:0016310 phosphorylation
• GO:0019303 D-ribose catabolic process
• GO:0046835 carbohydrate phosphorylation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:4xda, PDBe:4xda, PDBj:4xda
• PDBsum: 4xda
• PubMed: 25408351
• UniProt: A0A0H2UL04