Structure of PDB 5olk Chain A Binding Site BS02

Receptor Information
>5olk Chain A (length=395) Species: 398720 (Leeuwenhoekiella blandensis MED217) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EIKKIIKRDYSTAPFVLEKITNAIANAMAALGHGSEQDAKLISMQVYESL
LNNKEQESEYIPTVEQVQDMVEDKLMSSEFHDVAKAYIIYRNKRALERKT
NIFEKRINLKPYEYPELNEYVAAIRHSYWIHTEFNFTSDIQDFKTGLSEV
ERSAIKNTMLAISQIEVAVKTFWGDVHHRLPKPEIAAVGATFAESEVRHH
DAYSHLLEILGLNEEFKELKKKPVIMKRVHYLETSLKHAKSDDDREYTES
ILLFALFIEHVSLFSQFLIIMAFNKHKNMLKGISNAVEATSKEEQIHGDF
GVDIINIIKKENPEWFDEEHNNLIKEMCLNSFEAESKVVDWIFEKGELDF
LPKAVINEFLKNRFNKSLEAIGLEKLFDIDEALLQETEWFDDEII
Ligand information
Ligand IDDTP
InChIInChI=1S/C10H16N5O12P3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(25-7)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H,22,23)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
InChIKeySUYVUBYJARFZHO-RRKCRQDMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O3
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
FormulaC10 H16 N5 O12 P3
Name2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
ChEMBLCHEMBL335538
DrugBankDB03222
ZINCZINC000008215662
PDB chain5olk Chain A Residue 1002 [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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PDB5olk Novel ATP-cone-driven allosteric regulation of ribonucleotide reductase via the radical-generating subunit.
Resolution2.45 Å
Binding residue
(original residue number in PDB)		R12 A27 N30 A31 A90 Y91 Y94 R98 R102
Binding residue
(residue number reindexed from 1)		R8 A23 N26 A27 A86 Y87 Y90 R94 R98
Annotation score4
Binding affinityMOAD: Kd=1uM
PDBbind-CN: -logKd/Ki=6.00,Kd=1uM
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
GO:0046872 metal ion binding
Biological Process
GO:0009263 deoxyribonucleotide biosynthetic process

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:5olk, PDBe:5olk, PDBj:5olk
PDBsum5olk
PubMed29388911
UniProtA3XHF9

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