Structure of PDB 8vhp Chain H Binding Site BS05

Receptor Information

>8vhp Chain H (length=735) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

NQNLLVTKRDGSTERINLDKIHRVLDAAAEGLHNVSISQVELRSHIQFYD
GIKTSDIHETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPPA
LYDHVVKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHDRDMTFSYAAVKQL
EGKYLVQNRVTGEIYESAQFLYILVAACLFSNYPRETRLQYVKRFYDAVS
TFKISLPTPIMSGVRTPTRQFSSCVLIECGDSLDSINATSSAIVKYVSQR
AGIGINAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGVRGGA
ATLFYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGE
DITLFSPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSL
MMQERASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLEIALPTKPLND
VNDENGEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPIP
AAKRGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYYL
LKASNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWEA
LRESIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDGI
LRQVVPDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDP
SRFPSGKVPMQQLLKDLLTAYKFGVKTLYYQNTRD

Ligand information

Ligand ID

CDP

InChI

InChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1

InChIKey

ZWIADYZPOWUWEW-XVFCMESISA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341	NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
ACDLabs 10.04	O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
OpenEye OEToolkits 1.5.0	C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341	NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O

Formula

C9 H15 N3 O11 P2

Name

CYTIDINE-5'-DIPHOSPHATE

PDB chain

8vhp Chain H Residue 808 [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)	P208 T209 C225 G253 Q294 R298 N437 L438 E441 L464 M620 S622 S625
Binding residue (residue number reindexed from 1)	P207 T208 C224 G252 Q293 R297 N436 L437 E440 L463 M619 S621 S624
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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