Structure of PDB 7p9i Chain A Binding Site BS02

Receptor Information
>7p9i Chain A (length=271) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SYRHSFHAGNHADVLKHTVQSLIIESLKEKDKPFLYLDTHAGAGRYQLTG
EYLEGIARIWQQDDLPAELEAYINVVKHFNRSGQLRYYPGSPLIARQLLR
EQDSLQLTELHPSDYPLLRSEFQKDSRARVEKADGFQQLKAKLPPVSRRG
LILIDPPYEMKTDYQAVVSGIAEGYKRFATGTYALWYPVVLRQQIKRMIH
DLEATGIRKILQIELAVLPDSDRRGMTASGMIVINPPWKLEQQMNNVLPW
LHSKLVPAGTGHATVSWIVPE
Ligand information
Ligand ID6D6
InChIInChI=1S/C17H28N8O5/c18-3-1-4-24(5-2-9(19)17(28)29)6-10-12(26)13(27)16(30-10)25-8-23-11-14(20)21-7-22-15(11)25/h7-10,12-13,16,26-27H,1-6,18-19H2,(H,28,29)(H2,20,21,22)/t9-,10+,12+,13+,16+/m0/s1
InChIKeyNHAKJKNYYCYZBR-UOYPZJKHSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C(CCN(CCC(C(O)=O)N)CC1C(O)C(C(O1)n2cnc3c2ncnc3N)O)N
CACTVS 3.385NCCCN(CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 2.0.4c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CN(CCCN)CCC(C(=O)O)N)O)O)N
CACTVS 3.385NCCCN(CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 2.0.4c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CN(CCCN)CC[C@@H](C(=O)O)N)O)O)N
FormulaC17 H28 N8 O5
Name5'-{[(3S)-3-amino-3-carboxypropyl](3-aminopropyl)amino}-5'-deoxyadenosine
ChEMBLCHEMBL3414628
DrugBank
ZINCZINC000199753701
PDB chain7p9i Chain D Residue 101 [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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PDB7p9i Synthesis of RNA-cofactor conjugates and structural exploration of RNA recognition by an m6A RNA methyltransferase.
Resolution1.594 Å
Binding residue
(original residue number in PDB)		K18 H42 A43 G44 Y48 G99 S100 E118 D123 D164 P165 P166 E168 W195
Binding residue
(residue number reindexed from 1)		K16 H40 A41 G42 Y46 G90 S91 E109 D114 D155 P156 P157 E159 W186
Annotation score3
Enzymatic activity
Enzyme Commision number 2.1.1.266: 23S rRNA (adenine(2030)-N(6))-methyltransferase.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0008649 rRNA methyltransferase activity
GO:0008988 rRNA (adenine-N6-)-methyltransferase activity
GO:0036307 23S rRNA (adenine(2030)-N(6))-methyltransferase activity
Biological Process
GO:0006364 rRNA processing
GO:0015976 carbon utilization
GO:0032259 methylation
GO:0070475 rRNA base methylation
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7p9i, PDBe:7p9i, PDBj:7p9i
PDBsum7p9i
PubMed35580049
UniProtP37634|RLMJ_ECOLI Ribosomal RNA large subunit methyltransferase J (Gene Name=rlmJ)

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