Structure of PDB 8vhu Chain B Binding Site BS02

Receptor Information

>8vhu Chain B (length=719) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

LDKIHRVLDWAAEGLHNVSISQVELRSHIQFDIHETIIKAAADLISRDAP
DYQYLAARLAIFHLRKKAYGQFEPPALYDHVVKMVEMGKYDNHLLEDYTE
EEFKQMDTFIDHDRDMTFSYAAVKQLEGKYLVQNRVTGEIYESAQFLYIL
VAACLFSNYPRETRLQYVKRFYDAVSTFKISLPTPIMSGVRTPTRQFSSC
VLIECGDSLDSINATSSAIVKYVSQRAGIGINAGRIRALGSPIRGGEAFH
TGCIPFYKHFQTAVKSCSQGGAATLFYPMWHLEVESLLVLKNNRGVEGNR
VRHMDYGVQINKLMYTRLLKGEDITLFSPSDVPGLYDAFFADQEEFERLY
TKYEKDDSIRKQRVKAVELFSLMMQERASTGRIYIQNVDHCNTHSPFDPA
IAPVRQSNLCLEIALPTKPLNDVNDENGEIALCTLSAFNLGAINNLDELE
ELAILAVRALDALLDYQDYPIPAAKRGAMGRRTLGIGVINFAYYLAKHGK
RYSDGSANNLTHKTFEAIQYYLLKASNELAKEQGACPWFNETTYAKGILP
IDTYKKDLDTIANEPLHYDWEALRESIKTHGLRNSTLSALMPSETSSQIS
NATNGIEPPRGYVSIKASKDGILRQVVPDYEHLHDAYELLWEMPGNDGYL
QLVGIMQKFIDQSISANTNYDPSRFPSGKVPMQQLLKDLLTAYKFGVKTL
YYQNTRDGVDTDDLSNFQL

Ligand information

Ligand ID

DTP

InChI

InChI=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

InChIKey

SUYVUBYJARFZHO-RRKCRQDMSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	c1nc(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 3.341	Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N
CACTVS 3.341	Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O3
ACDLabs 10.04	O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O

Formula

C10 H16 N5 O12 P3

Name

2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

PDB chain

8vhu Chain B Residue 1401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	8vhu How ATP and dATP Act as Molecular Switches to Regulate Enzymatic Activity in the Prototypical Bacterial Class Ia Ribonucleotide Reductase.
Resolution	2.1 Å
Binding residue (original residue number in PDB)	D232 S233 L234 R262 I268 R269 H275
Binding residue (residue number reindexed from 1)	D207 S208 L209 R237 I243 R244 H250
Annotation score	1

External links

PDB	RCSB:8vhu, PDBe:8vhu, PDBj:8vhu
PDBsum	8vhu
PubMed	39164005
UniProt	P00452\|RIR1_ECOLI Ribonucleoside-diphosphate reductase 1 subunit alpha (Gene Name=nrdA); P69924\|RIR2_ECOLI Ribonucleoside-diphosphate reductase 1 subunit beta (Gene Name=nrdB)

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