Structure of PDB 7pd3 Chain x Binding Site BS02

Receptor Information
>7pd3 Chain x (length=366) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATVPRRHRYKKKWAATEPKFPAVRLALQNFDMTYSVQFGDLWPSIRVSLL
SEQKYGALVNNFAAWDHVSAKLEQLSAKDFVNEAISHWELQSEGGQSAAP
SPASWACSPNLRCFTFDRGDISRFPPARPGSLGVMEYYLMDAASLLPVLA
LGLQPGDIVLDLCAAPGGKTLALLQTGCCRNLAANDLSPSRIARLQKILH
SYVPEEIRDGNQVRVTSWDGRKWGELEGDTYDRVLVDVPCTTDRHSLHEE
ENNIFKRSRKKERQILPVLQVQLLAAGLLATKPGGHVVYSTCSLSHLQNE
YVVQGAIELLANQYSIQVQVEDLTHFRRVFMDTFCFFSSCQVGELVIPNL
MANFGPMYFCKMRRLT
Ligand information
Ligand IDSAM
InChIInChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
InChIKeyMEFKEPWMEQBLKI-FCKMPRQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
ACDLabs 10.04[O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H22 N6 O5 S
NameS-ADENOSYLMETHIONINE
ChEMBLCHEMBL1235831
DrugBank
ZINC
PDB chain7pd3 Chain x 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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PDB7pd3 Visualizing formation of the active site in the mitochondrial ribosome.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		C181 A183 P184 K187 D204 R209 G238 R239 D255 V256 P257 L291
Binding residue
(residue number reindexed from 1)		C163 A165 P166 K169 D186 R191 G220 R221 D237 V238 P239 L273
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.1.-
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0008173 RNA methyltransferase activity
GO:0008649 rRNA methyltransferase activity
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity
GO:0009383 rRNA (cytosine-C5-)-methyltransferase activity
GO:0016428 tRNA (cytidine-5-)-methyltransferase activity
GO:0019843 rRNA binding
Biological Process
GO:0001510 RNA methylation
GO:0006364 rRNA processing
GO:0031167 rRNA methylation
GO:0032259 methylation
GO:0042254 ribosome biogenesis
Cellular Component
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0005762 mitochondrial large ribosomal subunit

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7pd3, PDBe:7pd3, PDBj:7pd3
PDBsum7pd3
PubMed34609277
UniProtQ96CB9|NSUN4_HUMAN 5-methylcytosine rRNA methyltransferase NSUN4 (Gene Name=NSUN4)

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