Structure of PDB 4jal Chain A Binding Site BS01

Receptor Information
>4jal Chain A (length=156) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MALNIVLYEPEIPPNTGNIIRLCANTGFRLHIIEPMGFAWDDKRLRRAGL
DYHEFTAVTRHHDYRAFLEAENPQRLFALTTKGTPAHSAVSYQDGDYLMF
GPETRGLPASILDALPAEQKIRIPMVPDSRSMNLSNAVSVVVYEAWRQLG
YPGAVL
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 chain4jal Chain A Residue 201 [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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PDB4jal The tRNA recognition mechanism of the minimalist SPOUT methyltransferase, TrmL
Resolution2.0 Å
Binding residue
(original residue number in PDB)		L78 T79 T80 G100 E102 R121 I122 M124 M131 N132 L133
Binding residue
(residue number reindexed from 1)		L79 T80 T81 G101 E103 R122 I123 M125 M132 N133 L134
Annotation score5
Binding affinityPDBbind-CN: -logKd/Ki=4.60,Kd=25uM
Enzymatic activity
Enzyme Commision number 2.1.1.207: tRNA (cytidine(34)-2'-O)-methyltransferase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0008168 methyltransferase activity
GO:0008173 RNA methyltransferase activity
GO:0008175 tRNA methyltransferase activity
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity
GO:0042803 protein homodimerization activity
GO:0141098 tRNA (cytidine(34)-2'-O)-methyltransferase activity
GO:0141102 tRNA (5-carboxymethylaminomethyluridine(34)-2'-O)-methyltransferase activity
Biological Process
GO:0001510 RNA methylation
GO:0002131 wobble position cytosine ribose methylation
GO:0002132 wobble position uridine ribose methylation
GO:0006396 RNA processing
GO:0008033 tRNA processing
GO:0030488 tRNA methylation
GO:0032259 methylation
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:4jal, PDBe:4jal, PDBj:4jal
PDBsum4jal
PubMed23804755
UniProtP0AGJ7|TRML_ECOLI tRNA (cytidine(34)-2'-O)-methyltransferase (Gene Name=trmL)

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