Structure of PDB 7pd3 Chain x

Receptor sequence

>7pd3x (length=366) Species: 9606 (Homo sapiens)

ATVPRRHRYKKKWAATEPKFPAVRLALQNFDMTYSVQFGDLWPSIRVSLL
SEQKYGALVNNFAAWDHVSAKLEQLSAKDFVNEAISHWELQSEGGQSAAP
SPASWACSPNLRCFTFDRGDISRFPPARPGSLGVMEYYLMDAASLLPVLA
LGLQPGDIVLDLCAAPGGKTLALLQTGCCRNLAANDLSPSRIARLQKILH
SYVPEEIRDGNQVRVTSWDGRKWGELEGDTYDRVLVDVPCTTDRHSLHEE
ENNIFKRSRKKERQILPVLQVQLLAAGLLATKPGGHVVYSTCSLSHLQNE
YVVQGAIELLANQYSIQVQVEDLTHFRRVFMDTFCFFSSCQVGELVIPNL
MANFGPMYFCKMRRLT

3D structure

• PDB: 7pd3 Visualizing formation of the active site in the mitochondrial ribosome.
• Chain: x
• Resolution: 3.4 Å

Enzymatic activity

• Enzyme Commision number: 2.1.1.-

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	x	R26 K29 K37 P207 S208 K215 S276	R8 K11 K19 P189 S190 K197 S258
BS02	SAM	x	C181 A183 P184 K187 D204 R209 G238 R239 D255 V256 P257 L291	C163 A165 P166 K169 D186 R191 G220 R221 D237 V238 P239 L273

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

External links

• PDB: RCSB:7pd3, PDBe:7pd3, PDBj:7pd3
• PDBsum: 7pd3
• PubMed: 34609277
• UniProt: Q96CB9|NSUN4_HUMAN 5-methylcytosine rRNA methyltransferase NSUN4 (Gene Name=NSUN4)