Structure of PDB 4w5j Chain A Binding Site BS01

Receptor Information
>4w5j Chain A (length=211) Species: 373153 (Streptococcus pneumoniae D39) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNLLIMGLPGAGKGTQAAKIVEQFHVAHISTGDMFRAAMANQTEMGVLAK
SYIDKGELVPDEVTNGIVKERLSQDDIKETGFLLDGYPRTIEQAHALDKT
LAELGIELEGIINIEVNPDSLLERLSGRIIHRVTGETFHKVFNPPVYKEE
DYYQREDDKPETVKRRLDVNIAQGEPIIAHYRAKGLVHDIEGNQDINDVF
SDIEKVLTNLK
Ligand information
Ligand IDAP5
InChIInChI=1S/C20H29N10O22P5/c21-15-9-17(25-3-23-15)29(5-27-9)19-13(33)11(31)7(47-19)1-45-53(35,36)49-55(39,40)51-57(43,44)52-56(41,42)50-54(37,38)46-2-8-12(32)14(34)20(48-8)30-6-28-10-16(22)24-4-26-18(10)30/h3-8,11-14,19-20,31-34H,1-2H2,(H,35,36)(H,37,38)(H,39,40)(H,41,42)(H,43,44)(H2,21,23,25)(H2,22,24,26)/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1
InChIKeyOIMACDRJUANHTJ-XPWFQUROSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P@](O)(=O)O[P@](O)(=O)O[P@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)[CH](O)[CH]3O
FormulaC20 H29 N10 O22 P5
NameBIS(ADENOSINE)-5'-PENTAPHOSPHATE
ChEMBLCHEMBL437508
DrugBankDB01717
ZINCZINC000096085195
PDB chain4w5j Chain A Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4w5j New crystal structures of adenylate kinase from Streptococcus pneumoniae D39 in two conformations.
Resolution1.65 Å
Binding residue
(original residue number in PDB)		P9 G10 G12 K13 G14 T15 T31 G32 F35 R36 I53 E57 V59 T64 G86 Y87 R89 Q93 R124 R128 T137 F138 H139 F142 R156 R167 I197
Binding residue
(residue number reindexed from 1)		P9 G10 G12 K13 G14 T15 T31 G32 F35 R36 I53 E57 V59 T64 G86 Y87 R89 Q93 R124 R128 T137 F138 H139 F142 R155 R166 I196
Annotation score4
Binding affinityPDBbind-CN: -logKd/Ki=7.24,Kd=57nM
Enzymatic activity
Catalytic site (original residue number in PDB) K13 R89 R128 R156 R167
Catalytic site (residue number reindexed from 1) K13 R89 R128 R155 R166
Enzyme Commision number 2.7.4.3: adenylate kinase.
Gene Ontology
Molecular Function
GO:0004017 adenylate kinase activity
GO:0004550 nucleoside diphosphate kinase activity
GO:0005524 ATP 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:0009123 nucleoside monophosphate metabolic process
GO:0009132 nucleoside diphosphate metabolic process
GO:0009165 nucleotide biosynthetic process
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:4w5j, PDBe:4w5j, PDBj:4w5j
PDBsum4w5j
PubMed25372811
UniProtQ04ML5|KAD_STRP2 Adenylate kinase (Gene Name=adk)

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