Structure of PDB 3in1 Chain A Binding Site BS01

Receptor Information
>3in1 Chain A (length=312) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NLDVICIGAAIVDIPLQPVSKNIFDVDSYPLERIAMTTGGDAINEATIIS
RLGHRTALMSRIGKDAAGQFILDHCRKENIDIQSLKQDVSIDTSINVGLV
TEDGERTFVTNRNGSLWKLNIDDVDFARFSQAKLLSLASIFNSPLLDGKA
LTEIFTQAKARQMIICADMIKPRLNETLDDICEALSYVDYLFPNFAEAKL
LTGKETLDEIADCFLACGVKTVVIKTGKDGCFIKRGDMTMKVPAVAGITA
IDTIGAGDNFASGFIAALLEGKNLRECARFANATAAISVLSVGATTGVKN
RKLVEQLLEEYE
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 chain3in1 Chain A Residue 510 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3in1 Crystal structure of a putative Ribokinase in complex with ADP from E.coli
Resolution2.15 Å
Binding residue
(original residue number in PDB)		N196 K227 G229 G232 A246 T255 N284 A287
Binding residue
(residue number reindexed from 1)		N194 K225 G227 G230 A244 T253 N282 A285
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) R108 G257 A258 G259 D260
Catalytic site (residue number reindexed from 1) R106 G255 A256 G257 D258
Enzyme Commision number 2.7.1.-
Gene Ontology
Molecular Function
GO:0008673 2-dehydro-3-deoxygluconokinase activity
GO:0016301 kinase activity
GO:0016772 transferase activity, transferring phosphorus-containing groups
GO:0019200 carbohydrate kinase activity
GO:0042803 protein homodimerization activity
Biological Process
GO:0006974 DNA damage response
GO:0016310 phosphorylation
GO:0019698 D-galacturonate catabolic process
GO:0042840 D-glucuronate catabolic process
GO:0046835 carbohydrate phosphorylation
Cellular Component
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:3in1, PDBe:3in1, PDBj:3in1
PDBsum3in1
PubMed
UniProtP77493|YDJH_ECOLI Uncharacterized sugar kinase YdjH (Gene Name=ydjH)

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