Structure of PDB 4jl5 Chain A Binding Site BS01

Receptor Information
>4jl5 Chain A (length=203) Species: 224324 (Aquifex aeolicus VF5) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MILVFLGPPGAGKGTQAKRLAKEKGFVHISTGDILREAVQKGTPLGKKAK
EYMERGELVPDDLIIALIEEVFPKHGNVIFDGFPRTVKQAEALDEMLEKK
GLKVDHVLLFEVPDEVVIERLSGRRINPETGEVYHVKYNPPPPGVKVIQR
EDDKPEVIKKRLEVYREQTAPLIEYYKKKGILRIIDASKPVEEVYRQVLE
VIG
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 chain4jl5 Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4jl5 The energy landscape of adenylate kinase during catalysis.
Resolution1.24 Å
Binding residue
(original residue number in PDB)		G10 G12 K13 G14 T15 R120 R124 V133 Y134 H135 Y138 V191
Binding residue
(residue number reindexed from 1)		G10 G12 K13 G14 T15 R120 R124 V133 Y134 H135 Y138 V191
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K13 R85 R124 R150 R161
Catalytic site (residue number reindexed from 1) K13 R85 R124 R150 R161
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
GO:0043231 intracellular membrane-bounded organelle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4jl5, PDBe:4jl5, PDBj:4jl5
PDBsum4jl5
PubMed25580578
UniProtO66490|KAD_AQUAE Adenylate kinase (Gene Name=adk)

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