Structure of PDB 4erm Chain C Binding Site BS03

Receptor Information
>4erm Chain C (length=731) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VTKRDGSTERINLDKIHRVLDWAAEGLHNVSISQVELRSHIQFYDGIKTS
DIHETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPPALYDHV
VKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHDRDMTFSYAAVKQLEGKYL
VQNRVTGEIYESAQFLYILVAACLFSNYPRETRLQYVKRFYDAVSTFKIS
LPTPIMSGVRTPTRQFSSCVLIECGDSLDSINATSSAIVKYVSQRAGIGI
NAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGVRGGAATLFY
PMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGEDITLF
SPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSLMMQER
ASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLEIALPTKPLNDVNDEN
GEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPIPAAKRG
AMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYYLLKASN
ELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWEALRESI
KTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDGILRQVV
PDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPSRFPS
GKVPMQQLLKDLLTAYKFGVKTLYYQNTRDG
Ligand information
Ligand IDDTP
InChIInChI=1S/C10H16N5O12P3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(25-7)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H,22,23)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
InChIKeySUYVUBYJARFZHO-RRKCRQDMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O3
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
FormulaC10 H16 N5 O12 P3
Name2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
ChEMBLCHEMBL335538
DrugBankDB03222
ZINCZINC000008215662
PDB chain4erm Chain C Residue 803 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4erm Tangled up in knots: structures of inactivated forms of E. coli class Ia ribonucleotide reductase.
Resolution3.95 Å
Binding residue
(original residue number in PDB)		D232 S233 L234 R262 I268 R269 H275 T276
Binding residue
(residue number reindexed from 1)		D226 S227 L228 R256 I262 R263 H269 T270
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) C219 N431 C433 E435 C456 Y724 Y725
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:4erm, PDBe:4erm, PDBj:4erm
PDBsum4erm
PubMed22727814
UniProtP00452|RIR1_ECOLI Ribonucleoside-diphosphate reductase 1 subunit alpha (Gene Name=nrdA)

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