Structure of PDB 8p28 Chain A Binding Site BS03

Receptor Information
>8p28 Chain A (length=645) Species: 165179 (Segatella copri) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIQTVVKRDGRIVGFNEQKIMAAIRKAMLHTDKGEDTTLIEQITDHISYR
GKSQMSVEAIQDAIEMELMKSARKDVAQKYIAYRNQRNIARKAKTRDVFM
SDTPAGMMMKFASETTKPFVDDYLLSEDVRDAVMHNYIHIHDKDYYPTKS
LTCVQHPLDVILNHGFTAGHGSSRPAKRIETAAVLACISLETCQNEMHGG
QAIPAFDFYLAPYVRMSYQEEVKNLEKLTGEDLSNLYDAPIDDYIEKPLD
GLQGRERLEQHAINKTVNRVHQAMEAFIHNMNTIHSRVFSSINYGTDTSA
EGRCIMREILQSTYQGVGNGETAIFPIQIWKKKRGVNYLPEDRNYDLYKL
ACKVTARRFFPNFLNLDATFNQNEKWRADDPERYKWEIATMGCRTRVFED
RWGEKTSIARGNLSFSTINIVKLAIECMGIENEKQRIDMFFAKLDNILDI
TAKQLDERFQFQKTAMAKQFPLLMKYLWVGAENLKPEETIESVINHGTLG
IGFIGLAECLVALIGKHHGESEKAQELGLKIITYMRDRANEFSEQYHHNY
SILATPAEGLSGKFTKKDRKQFGVIPGVTDRDYYTNSNHVPVYYKCTALK
KAQIEAPYHDLTRGGHIFYVEINPSVIESVVDMMDKYNMGYGSVN
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 chain8p28 Chain A Residue 803 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8p28 Activity modulation in anaerobic ribonucleotide reductase: nucleotide binding to the ATP-cone mediates long-range order-disorder transitions in the active site
Resolution2.77 Å
Binding residue
(original residue number in PDB)		R8 A23 K26 H30 Y80 Y83 R87 R91
Binding residue
(residue number reindexed from 1)		R8 A23 K26 H30 Y80 Y83 R87 R91
Annotation score1
Enzymatic activity
Enzyme Commision number 1.17.4.2: ribonucleoside-triphosphate reductase (thioredoxin).
Gene Ontology
Molecular Function
GO:0004748 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
GO:0005524 ATP binding
GO:0008998 ribonucleoside-triphosphate reductase (thioredoxin) activity
GO:0016491 oxidoreductase activity
Biological Process
GO:0006260 DNA replication
GO:0009265 2'-deoxyribonucleotide biosynthetic process
Cellular Component
GO:0031250 anaerobic ribonucleoside-triphosphate reductase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8p28, PDBe:8p28, PDBj:8p28
PDBsum8p28
PubMed38968292
UniProtA0A3E4SF67

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