Structure of PDB 5cnv Chain A Binding Site BS01

Receptor Information
>5cnv Chain A (length=736) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNQNLLVTKRDGSTERINLDKIHRVLDWAAEGLHNVSISQVELRSHIQFY
DGIKTSDIHETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPP
ALYDHVVKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHDRDMTFSYAAVKQ
LEGKYLVQNRVTGEIYESAQFLYILVAACLFSNYPRETRLQYVKRFYDAV
STFKISLPTPIMSGVRTPTRQFSSCVLIECGDSLDSINATSSAIVKYVSQ
RAGIGINAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGVRGG
AATLFYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKG
EDITLFSPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFS
LMMQERASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLEIALPTKPLN
DVNDENGEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPI
PAAKRGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYY
LLKASNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWE
ALRESIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDG
ILRQVVPDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYD
PSRFPSGKVPMQQLLKDLLTAYKFGVKTLYYQNTRD
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain5cnv Chain A Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5cnv Molecular basis for allosteric specificity regulation in class Ia ribonucleotide reductase from Escherichia coli.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		T209 S224 C225 G253 R298 G299 L438 E441 L464 P621 S622 T624 S625
Binding residue
(residue number reindexed from 1)		T209 S224 C225 G253 R298 G299 L438 E441 L464 P621 S622 T624 S625
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C225 N437 C439 E441 C462 Y730 Y731
Catalytic site (residue number reindexed from 1) C225 N437 C439 E441 C462 Y730 Y731
Enzyme Commision number 1.17.4.1: ribonucleoside-diphosphate reductase.
Gene Ontology
Molecular Function
GO:0004748 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016491 oxidoreductase activity
GO:0042802 identical protein binding
GO:0044183 protein folding chaperone
Biological Process
GO:0006457 protein folding
GO:0009185 ribonucleoside diphosphate metabolic process
GO:0009263 deoxyribonucleotide biosynthetic process
GO:0009265 2'-deoxyribonucleotide biosynthetic process
GO:0015949 nucleobase-containing small molecule interconversion
Cellular Component
GO:0005829 cytosol
GO:0005971 ribonucleoside-diphosphate reductase complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5cnv, PDBe:5cnv, PDBj:5cnv
PDBsum5cnv
PubMed26754917
UniProtP00452|RIR1_ECOLI Ribonucleoside-diphosphate reductase 1 subunit alpha (Gene Name=nrdA)

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