Structure of PDB 2r1r Chain B Binding Site BS02

Receptor Information
>2r1r 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 IDTTP
InChIInChI=1S/C10H17N2O14P3/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,21,22)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChIKeyNHVNXKFIZYSCEB-XLPZGREQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H17 N2 O14 P3
NameTHYMIDINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL363559
DrugBankDB02452
ZINCZINC000008215959
PDB chain2r1r Chain B Residue 762 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2r1r 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)		D232 S233 L234 R262 I268 R269 H275
Binding residue
(residue number reindexed from 1)		D228 S229 L230 R258 I264 R265 H271
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2r1r, PDBe:2r1r, PDBj:2r1r
PDBsum2r1r
PubMed9309223
UniProtP00452|RIR1_ECOLI Ribonucleoside-diphosphate reductase 1 subunit alpha (Gene Name=nrdA)

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