Structure of PDB 3r1r Chain B Binding Site BS02

Receptor Information
>3r1r Chain B (length=733) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LLVTKRDGSTERINLDKIHRVLDWAAEGLHNVSISQVELRSHIQFYDGIK
TSDIHETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPPALYD
HVVKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHDRDMTFSYAAVKQLEGK
YLVQNRVTGEIYESAQFLYILVAACLFSNYPRETRLQYVKRFYDAVSTFK
ISLPTPIMSGVRTPTRQFSSCVLIECGDSLDSINATSSAIVKYVSQRAGI
GINAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGVRGGAATL
FYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGEDIT
LFSPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSLMMQ
ERASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLEIALPTKPLNDVND
ENGEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPIPAAK
RGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYYLLKA
SNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWEALRE
SIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDGILRQ
VVPDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPSRF
PSGKVPMQQLLKDLLTAYKFGVKTLYYQNTRDG
Ligand information
Ligand IDATP
InChIInChI=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
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(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 3.341Nc1ncnc2n(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
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain3r1r Chain B Residue 762 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3r1r Binding of allosteric effectors to ribonucleotide reductase protein R1: reduction of active-site cysteines promotes substrate binding.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		K9 I17 N18 K21 I22 T55 H59 K91
Binding residue
(residue number reindexed from 1)		K5 I13 N14 K17 I18 T51 H55 K87
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) C221 N433 C435 E437 C458 Y726 Y727
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3r1r, PDBe:3r1r, PDBj:3r1r
PDBsum3r1r
PubMed9309223
UniProtP00452|RIR1_ECOLI Ribonucleoside-diphosphate reductase 1 subunit alpha (Gene Name=nrdA)

[Back to BioLiP]