Structure of PDB 8vhp Chain F Binding Site BS04

Receptor Information

>8vhp Chain F (length=732) 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
RESIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKKDGILRQ
VVPDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPSRF
PSGKVPMQQLLKDLLTAYKFGVKTLYYQNTRD

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 F Residue 807 [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)	D232 S233 L234 R262 I268 R269 H275 F281
Binding residue (residue number reindexed from 1)	D230 S231 L232 R260 I266 R267 H273 F279
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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