Structure of PDB 8vhq Chain B Binding Site BS02

Receptor Information

>8vhq Chain B (length=734) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

QNLLVTKRDGSTERINLDKIHRVLDAAAEGLHNVSISQVELRSHIQFYDG
IKTSDIHETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPPAL
YDHVVKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHDRDMTFSYAAVKQLE
GKYLVQNRVTGEIYESAQFLYILVAACLFSNYPRETRLQYVKRFYDAVST
FKISLPTPIMSGVRTPTRQFSSCVLIECGDSLDSINATSSAIVKYVSQRA
GIGINAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGVRGGAA
TLFYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGED
ITLFSPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSLM
MQERASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLEIALPTKPLNDV
NDENGEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPIPA
AKRGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYYLL
KASNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWEAL
RESIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDGIL
RQVVPDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPS
RFPSGKVPMQQLLKDLLTAYKFGVKTLYYQNTRD

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

8vhq Chain B Residue 801 [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	8vhq How ATP and dATP Act as Molecular Switches to Regulate Enzymatic Activity in the Prototypical Bacterial Class Ia Ribonucleotide Reductase.
Resolution	3.4 Å
Binding residue (original residue number in PDB)	V7 K9 R10 E15 I17 N18 I22 T55 H59
Binding residue (residue number reindexed from 1)	V5 K7 R8 E13 I15 N16 I20 T53 H57
Annotation score	1

External links

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

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