Structure of PDB 3kgd Chain D Binding Site BS01

Receptor Information
>3kgd Chain D (length=340) Species: 511145 (Escherichia coli str. K-12 substr. MG1655) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RHMKRMIALDGAQGEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLL
RQHLTAVKAATEICGATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSC
TLVLQTVLPALWFADGPSRVEVSGGTDNPSAPPADFIRRVLEPLLAKIGI
HQQTTLLRHGFYPAGGGVVATEVSPVASFNTLQLGERGNIVQMRGEVLLA
GVPRHVAEREIATLAGSFSLHEQNIHNLPRDQGPGNTVSLEVESENITER
FFVVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLADQLVLPMALAGAG
EFTVAHPSCHLLTNIAVVERFLPVRFSLIETDGVTRVSIE
Ligand information
Ligand IDAMP
InChIInChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyUDMBCSSLTHHNCD-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
ACDLabs 12.01O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
FormulaC10 H14 N5 O7 P
NameADENOSINE MONOPHOSPHATE
ChEMBLCHEMBL752
DrugBankDB00131
ZINCZINC000003860156
PDB chain3kgd Chain D Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3kgd Structure of the RNA 3'-phosphate cyclase-adenylate intermediate illuminates nucleotide specificity and covalent nucleotidyl transfer.
Resolution1.68 Å
Binding residue
(original residue number in PDB)		S129 A130 P131 F135 F251 Y284 D287 Q288 H309
Binding residue
(residue number reindexed from 1)		S130 A131 P132 F136 F252 Y285 D288 Q289 H310
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) E14 H309
Catalytic site (residue number reindexed from 1) E15 H310
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:3kgd, PDBe:3kgd, PDBj:3kgd
PDBsum3kgd
PubMed20399182
UniProtP46849|RTCA_ECOLI RNA 3'-terminal phosphate cyclase (Gene Name=rtcA)

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