Structure of PDB 1rkd Chain A Binding Site BS02

Receptor Information
>1rkd Chain A (length=306) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AGSLVVLGSINADHILNLQSFPTPGETVTGNHYQVAFGGKGANQAVAAGR
SGANIAFIACTGDDSIGESVRQQLATDNIDITPVSVIKGESTGVALIFVN
GEGENVIGIHAGANAALSPALVEAQRERIANASALLMQLESPLESVMAAA
KIAHQNKTIVALNPAPARELPDELLALVDIITPNETEAEKLTGIRVENDE
DAAKAAQVLHEKGIRTVLITLGSRGVWASVNGEGQRVPGFRVQAVDTIAA
GDTFNGALITALLEEKPLPEAIRFAHAAAAIAVTRKGAQPSVPWREEIDA
FLDRQR
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain1rkd Chain A Residue 310 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1rkd Structure of Escherichia coli ribokinase in complex with ribose and dinucleotide determined to 1.8 A resolution: insights into a new family of kinase structures.
Resolution1.84 Å
Binding residue
(original residue number in PDB)		T223 G225 G254 H279 A282
Binding residue
(residue number reindexed from 1)		T220 G222 G251 H276 A279
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) A252 A253 G254 D255
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:0042803 protein homodimerization 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:1rkd, PDBe:1rkd, PDBj:1rkd
PDBsum1rkd
PubMed9519409
UniProtP0A9J6|RBSK_ECOLI Ribokinase (Gene Name=rbsK)

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