Structure of PDB 8vhp Chain E Binding Site BS01

Receptor Information

>8vhp Chain E (length=733) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

NLLVTKRDGSTERINLDKIHRVLDAAAEGLHNVSISQVELRSHIQFYDGI
KTSDIHETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPPALY
DHVVKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHDRDMTFSYAAVKQLEG
KYLVQNRVTGEIYESAQFLYILVAACLFSNYPRETRLQYVKRFYDAVSTF
KISLPTPIMSGVRTPTRQFSSCVLIECGDSLDSINATSSAIVKYVSQRAG
IGINAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGVRGGAAT
LFYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGEDI
TLFSPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSLMM
QERASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLEIALPTKPLNDVN
DENGEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPIPAA
KRGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYYLLK
ASNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWEALR
ESIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDGILR
QVVPDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPSR
FPSGKVPMQQLLKDLLTAYKFGVKTLYYQNTRD

Ligand information

Ligand ID

ATP

InChI

InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1

InChIKey

ZKHQWZAMYRWXGA-KQYNXXCUSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341	Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04	O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341	Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O

Formula

C10 H16 N5 O13 P3

Name

ADENOSINE-5'-TRIPHOSPHATE

PDB chain

8vhp Chain E Residue 804 [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	8vhp How ATP and dATP Act as Molecular Switches to Regulate Enzymatic Activity in the Prototypical Bacterial Class Ia Ribonucleotide Reductase.
Resolution	2.608 Å
Binding residue (original residue number in PDB)	V7 K9 R10 E15 I17 N18 K21 I22 T55 H59 K91
Binding residue (residue number reindexed from 1)	V4 K6 R7 E12 I14 N15 K18 I19 T52 H56 K88
Annotation score	1

External links

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

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