Structure of PDB 4xda Chain A Binding Site BS01

Receptor Information
>4xda Chain A (length=306) Species: 345073 (Vibrio cholerae O395) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNKLVVLGSVNADHVLQVPSFPRPGETLHGRNYQVIPGGKGANQAVAAAR
MQADVGFIACVGDDSFGINIRESFKLDGINTAGVKLQPNCPTGIAMIQVS
DSGENSICISAEANAKLTAAAIEPDLAAIRDARYLLMQLETPLDGILKAA
QEAKTAKTNVILNPAPARELPDELLKCVDLITPNETEAEVLTGITVYDDS
SAQQAADALHCKGIEIVIITLGSKGVWLSQNGRGQRIPGFVVKATDTTAA
GDTFNGALVTGLLQEMPLESAIKFAHAAAAISVTRFGAQTSIPTRAEVEA
FLAEHS
Ligand information
Ligand IDRIB
InChIInChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4-,5+/m1/s1
InChIKeyHMFHBZSHGGEWLO-AIHAYLRMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(C1C(C(C(O1)O)O)O)O
CACTVS 3.341OC[CH]1O[CH](O)[CH](O)[CH]1O
CACTVS 3.341OC[C@H]1O[C@H](O)[C@H](O)[C@@H]1O
OpenEye OEToolkits 1.5.0C([C@@H]1[C@H]([C@H]([C@H](O1)O)O)O)O
ACDLabs 10.04OC1C(OC(O)C1O)CO
FormulaC5 H10 O5
Namealpha-D-ribofuranose;
alpha-D-ribose;
D-ribose;
ribose
ChEMBLCHEMBL606078
DrugBank
ZINCZINC000003860714
PDB chain4xda Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4xda Crystal Structure of Apo and Ligand Bound Vibrio cholerae Ribokinase (Vc-RK): Role of Monovalent Cation Induced Activation and Structural Flexibility in Sugar Phosphorylation
Resolution1.75 Å
Binding residue
(original residue number in PDB)		N11 D13 G39 K40 N43 A95 E140 D252
Binding residue
(residue number reindexed from 1)		N11 D13 G39 K40 N43 A95 E140 D252
Annotation score5
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.
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4xda, PDBe:4xda, PDBj:4xda
PDBsum4xda
PubMed25408351
UniProtA0A0H2UL04

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