Structure of PDB 2ytz Chain B Binding Site BS01

Receptor Information
>2ytz Chain B (length=365) Species: 53953 (Pyrococcus horikoshii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LIEVQEGKAKILIPDSPVFYNPRMALNRDIVVVLLNILNPKIVLDALSAT
GIRGIRFALETPAEEVWLNDISEDAYELMKRNVMLNFDGELRESKGRAIL
KGEKTIVINHDDANRLMAERHRYFHFIDLDPFGSPMEFLDTALRSAKRRG
ILGVTATDGAPLCGAHPRACLRKYLAVPLRGELCHEVGTRILVGVIARYA
AKYDLGIDVILAYYKDHYFRAFVKLKDGARKGDETLEKLGYIYFDDKTGK
FELEQGFLPTRPNAYGPVWLGPLKDEKIVSKMVKEAESLSLARKKQALKL
LKMIDQELDIPLFYDTHAIGRRETKKVEEIISALREQGYEATRTHFSPTG
IKTSAPYEVFIETIK
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 chain2ytz Chain B Residue 1002 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2ytz Crystal Structure of tRNA N(2),N(2)-Guanosine Dimethyltransferase Trm1 from Pyrococcus horikoshii
Resolution2.65 Å
Binding residue
(original residue number in PDB)		R36 L55 A57 R61 D78 I79 D120 A121 D138 F140 F146
Binding residue
(residue number reindexed from 1)		R28 L47 A49 R53 D70 I71 D112 A113 D130 F132 F138
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.1.216: tRNA (guanine(26)-N(2))-dimethyltransferase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0003723 RNA binding
GO:0008168 methyltransferase activity
GO:0016423 tRNA (guanine) methyltransferase activity
GO:0016740 transferase activity
GO:0160104 tRNA (guanine(26)-N2)-dimethyltransferase activity
Biological Process
GO:0002940 tRNA N2-guanine methylation
GO:0006400 tRNA modification
GO:0008033 tRNA processing
GO:0030488 tRNA methylation
GO:0032259 methylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2ytz, PDBe:2ytz, PDBj:2ytz
PDBsum2ytz
PubMed18789948
UniProtO59493|TRM1_PYRHO tRNA (guanine(26)-N(2))-dimethyltransferase (Gene Name=trm1)

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