Structure of PDB 3tw3 Chain A Binding Site BS01

Receptor Information
>3tw3 Chain A (length=336) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RMIALDGAQGEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLLRQHL
TAVKAATEICGATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVL
QTVLPALWFADGPSRVEVSGGTDNPSAPPADFIRRVLEPLLAKIGIHQQT
TLLRHGFYPAGGGVVATEVSPVASFNTLQLGERGNIVQMRGEVLLAGVPR
HVAEREIATLAGSFSLHEQNIHNLPRDQGPGNTVSLEVESENITERFFVV
GEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLADQLVLPMALAGAGEFTV
AHPSSNLLTNIAVVERFLPVRFSLIETDGVTRVSIE
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 chain3tw3 Chain A Residue 401 [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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PDB3tw3 Structures of RNA 3'-phosphate cyclase bound to ATP reveal the mechanism of nucleotidyl transfer and metal-assisted catalysis.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		E14 G16 G17 Q18 R21 R40 R43 S129 A130 P131 F135 F251 Y284 D287 Q288
Binding residue
(residue number reindexed from 1)		E11 G13 G14 Q15 R18 R37 R40 S126 A127 P128 F132 F248 Y281 D284 Q285
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) E14 N309
Catalytic site (residue number reindexed from 1) E11 N306
Enzyme Commision number 6.5.1.4: RNA 3'-terminal-phosphate cyclase (ATP).
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0003963 RNA-3'-phosphate cyclase activity
GO:0005524 ATP binding
GO:0016874 ligase activity
Biological Process
GO:0006396 RNA processing
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3tw3, PDBe:3tw3, PDBj:3tw3
PDBsum3tw3
PubMed22167800
UniProtP46849|RTCA_ECOLI RNA 3'-terminal phosphate cyclase (Gene Name=rtcA)

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