Structure of PDB 5olk Chain D Binding Site BS01

Receptor Information
>5olk Chain D (length=393) Species: 398720 (Leeuwenhoekiella blandensis MED217) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IKKIIKRDYSTAPFVLEKITNAIANAMAALGHGSEQDAKLISMQVYESLL
NNKEQESEYIPTVEQVQDMVEDKLMSSEFHDVAKAYIIYRNKRALERKTN
IFEKRINLKPYEYPELNEYVAAIRHSYWIHTEFNFTSDIQDFKTGLSEVE
RSAIKNTMLAISQIEVAVKTFWGDVHHRLPKPEIAAVGATFAESEVRHHD
AYSHLLEILGLNEEFKELKKKPVIMKRVHYLETSLKHAKSDDDREYTESI
LLFALFIEHVSLFSQFLIIMAFNKHKNMLKGISNAVEATSKEEQIHGDFG
VDIINIIKKENPEWFDEEHNNLIKEMCLNSFEAESKVVDWIFEKGELDFL
PKAVINEFLKNRFNKSLEAIGLEKLFDIDEALLQETEWFDDEI
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 D Residue 1001 [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)		I9 K11 R12 F19 V20 K23 I24 V68 V71 Q72
Binding residue
(residue number reindexed from 1)		I4 K6 R7 F14 V15 K18 I19 V63 V66 Q67
Annotation score4
Binding affinityMOAD: 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
View graph for
Biological Process
External links
PDB RCSB:5olk, PDBe:5olk, PDBj:5olk
PDBsum5olk
PubMed29388911
UniProtA3XHF9

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