Structure of PDB 8cbl Chain F Binding Site BS02

Receptor Information
>8cbl Chain F (length=294) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATREFIEMWRLLGREVPEHITEEELKTLMECVSNTAKKKYLKYLYTKEKV
KKARQIKKEMKAAAREEAKNIKLLETTEEDKQKNFLFLRLWDRNMDIAMG
WKGAQAMQFGQPLVFDMAYENYMKRKELQNTVSQLLESEGWNRRNVDPFH
IYFCNLKIDGALHRELVKRYQEKWDKLLLTSTEKSHVDLFPKDSIIYLTA
DSPNVMTTFRHDKVYVIGSFVDKSMQPGTSLAKAKRLNLATECLPLDKYL
QWEIGNKNLTLDQMIRILLCLKNNGNWQEALQFVPKRKHTGFLE
Ligand information
Ligand IDSAH
InChIInChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
InChIKeyZJUKTBDSGOFHSH-WFMPWKQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
CACTVS 3.341N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
ACDLabs 10.04O=C(O)C(N)CCSCC3OC(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)CSCC[C@@H](C(=O)O)N)O)O)N
FormulaC14 H20 N6 O5 S
NameS-ADENOSYL-L-HOMOCYSTEINE
ChEMBLCHEMBL418052
DrugBankDB01752
ZINCZINC000004228232
PDB chain8cbl Chain F Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8cbl Structural basis for human mitochondrial tRNA maturation.
Resolution2.79 Å
Binding residue
(original residue number in PDB)		L290 T291 A292 I309 G310 F312 D314 T321 S322 L336 N350 L351 M356
Binding residue
(residue number reindexed from 1)		L198 T199 A200 I217 G218 F220 D222 T229 S230 L244 N258 L259 M264
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.1.-
2.1.1.218: tRNA (adenine(9)-N(1))-methyltransferase.
2.1.1.221: tRNA (guanine(9)-N(1))-methyltransferase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0042802 identical protein binding
GO:0052905 tRNA (guanosine(9)-N1)-methyltransferase activity
GO:0160106 tRNA (adenine(9)-N1)-methyltransferase activity
Biological Process
GO:0000964 mitochondrial RNA 5'-end processing
GO:0006397 mRNA processing
GO:0008033 tRNA processing
GO:0032259 methylation
GO:0070131 positive regulation of mitochondrial translation
GO:0070901 mitochondrial tRNA methylation
GO:0090646 mitochondrial tRNA processing
GO:0097745 mitochondrial tRNA 5'-end processing
GO:1990180 mitochondrial tRNA 3'-end processing
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0030678 mitochondrial ribonuclease P complex
GO:0042645 mitochondrial nucleoid
GO:0043527 tRNA methyltransferase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8cbl, PDBe:8cbl, PDBj:8cbl
PDBsum8cbl
PubMed38824131
UniProtQ7L0Y3|TM10C_HUMAN tRNA methyltransferase 10 homolog C (Gene Name=TRMT10C)

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