Structure of PDB 7apu Chain B Binding Site BS01

Receptor Information
>7apu Chain B (length=214) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAK
DIMDAGKLVTDELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAG
INVDYVLEFDVPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTG
EELTTRKDDQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDGTK
PVAEVRADLEKILG
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 chain7apu Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7apu Dynamic Connection between Enzymatic Catalysis and Collective Protein Motions.
Resolution1.36 Å
Binding residue
(original residue number in PDB)		G10 G12 K13 G14 T15 R119 R123 Y133 H134 F137 V202
Binding residue
(residue number reindexed from 1)		G10 G12 K13 G14 T15 R119 R123 Y133 H134 F137 V202
Annotation score5
Enzymatic activity
Enzyme Commision number 2.7.4.3: adenylate kinase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004017 adenylate kinase activity
GO:0004550 nucleoside diphosphate kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016208 AMP binding
GO:0016301 kinase activity
GO:0016776 phosphotransferase activity, phosphate group as acceptor
GO:0019205 nucleobase-containing compound kinase activity
GO:0050145 nucleoside monophosphate kinase activity
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006172 ADP biosynthetic process
GO:0009123 nucleoside monophosphate metabolic process
GO:0009132 nucleoside diphosphate metabolic process
GO:0009165 nucleotide biosynthetic process
GO:0015951 purine ribonucleotide interconversion
GO:0016310 phosphorylation
GO:0044209 AMP salvage
GO:0046940 nucleoside monophosphate 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:7apu, PDBe:7apu, PDBj:7apu
PDBsum7apu
PubMed34250801
UniProtP69441|KAD_ECOLI Adenylate kinase (Gene Name=adk)

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