Structure of PDB 8p28 Chain B Binding Site BS04

Receptor Information
>8p28 Chain B (length=647) Species: 165179 (Segatella copri) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIQTVVKRDGRIVGFNEQKIMAAIRKAMLHTDKGEDTTLIEQITDHISYR
GKSQMSVEAIQDAIEMELMKSARKDVAQKYIAYRNQRNIARKAKTRDVFM
SIVDTPAGMMMKFASETTKPFVDDYLLSEDVRDAVMHNYIHIHDKDYYPT
KSLTCVQHPLDVILNHGFTAGHGSSRPAKRIETAAVLACISLETCQNEMH
GGQAIPAFDFYLAPYVRMSYQEEVKNLEKLTGEDLSNLYDAPIDDYIEKP
LDGLQGRERLEQHAINKTVNRVHQAMEAFIHNMNTIHSRVFSSINYGTDT
SAEGRCIMREILQSTYQGVGNGETAIFPIQIWKKKRGVNYLPEDRNYDLY
KLACKVTARRFFPNFLNLDATFNQNEKWRADDPERYKWEIATMGCRTRVF
EDRWGEKTSIARGNLSFSTINIVKLAIECMGIENEKQRIDMFFAKLDNIL
DITAKQLDERFQFQKTAMAKQFPLLMKYLWVGAENLKPEETIESVINHGT
LGIGFIGLAECLVALIGKHHGESEKAQELGLKIITYMRDRANEFSEQYHH
NYSILATPAEGLSGKFTKKDRKQFGVIPGVTDRDYYTNSNHVPVYYKCTA
LKKAQIEAPYHDLTRGGHIFYVEINPSVIESVVDMMDKYNMGYGSVN
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 B 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)		K79 Y80 Y83 R91
Binding residue
(residue number reindexed from 1)		K79 Y80 Y83 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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