Structure of PDB 7agj Chain B Binding Site BS01

Receptor Information
>7agj Chain B (length=721) Species: 224324 (Aquifex aeolicus VF5) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MYVIKRSGRKEKLDINKIRIAIKFACEGLNVDPLELEADAQIQFRDGITT
KEIQQLLIKTAAEKVSAERPDWTYTAARLLLYDLYKDVAHLRGYSLRDDL
GKYKPYNRKNFYSFVKEYVEKGIYGEYLLENYSEEDFNKLANYIKPERDL
YFTYTGIKILYDRYLVRDEEGRVIELPQEMYMLIAMTLAVPEKPEERLKW
AKKFYDVLSEHKVTVATPTLMNARRPFTQLSSCFVLTVDDDLFDIFDNVK
KAGMISKFAGGLGVYLGKIRATVIPVVKLINDTMTYVSASITLDIWHKDI
LDFLEVKTHDIHPAVSIPDLFMKRLKNREDWTLIDPYWARQYITRKIEPK
GLEDFYGEEFEKWYLELEENLPSYAKKKVNSFELWKRLLTVAFETGEPYI
FFRDEANRKNPNKHTGMVYSSNLCHEIVQTMSPSKHEKPVLDPETGEITY
KKEAGDLPVCNLGSVNLGKVHTEEEIKEVLPLLVRMLDNVIEMNFYAIPE
AEYTNKRYRAIGIGVSNYHYCLVKNGIKWESEEHLKFADKLFELIAFYAL
KGSLELAKERGRYKLFDGSNWSKGILFGRSVEEIEENSRQNGNNLPWREL
AEEIKKYGIRNAYLLALMPTGSTSLILGATPSIDPIFARFYKEILPQVPP
EVDRFYWHYKTAYTIDHEWTIRAAAVRQKWIDQAQSLNLFVDPQNIDGPR
LSRLYELAWELGLKTIYYLRS
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-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)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
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)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)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain7agj Chain B Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7agj Structural and Biochemical Investigation of Class I Ribonucleotide Reductase from the Hyperthermophile Aquifex aeolicus.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		V5 K7 R8 E13 D16 K19 I20 T52 Q56 K88
Binding residue
(residue number reindexed from 1)		V3 K5 R6 E11 D14 K17 I18 T50 Q54 K86
Annotation score1
Enzymatic activity
Enzyme Commision number 1.17.4.1: ribonucleoside-diphosphate reductase.
Gene Ontology
Molecular Function
GO:0004748 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
GO:0005524 ATP binding
GO:0016491 oxidoreductase activity
Biological Process
GO:0009263 deoxyribonucleotide biosynthetic process
Cellular Component
GO:0005971 ribonucleoside-diphosphate reductase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7agj, PDBe:7agj, PDBj:7agj
PDBsum7agj
PubMed34941255
UniProtO66503|RIR1_AQUAE Ribonucleoside-diphosphate reductase subunit alpha (Gene Name=nrdA)

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