Structure of PDB 1p9p Chain A Binding Site BS01

Receptor Information
>1p9p Chain A (length=235) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MWIGIISLFPEMFRAITDYGVTGRAVKNGLLSIQSWSPRDFTHDRHRTVD
DRPYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVS
ELATNQKLILVCGRYEGIDERVIQTEIDEEWSIGDYVLSGGELPAMTLID
SVSRFIPGVLGEGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQ
SLGRTWLRRPELLENLALTEEQARLLAEFKTEHAQ
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 chain1p9p Chain A Residue 300 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1p9p Insights into Catalysis by a Knotted TrmD tRNA Methyltransferase.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		Y86 L87 S88 P89 Q90 G113 Y115 I133 L138 G140 G141 P144
Binding residue
(residue number reindexed from 1)		Y86 L87 S88 P89 Q90 G113 Y115 I133 L138 G140 G141 P144
Annotation score5
Binding affinityMOAD: Kd=68nM
Enzymatic activity
Catalytic site (original residue number in PDB) P89 E116 R154
Catalytic site (residue number reindexed from 1) P89 E116 R154
Enzyme Commision number 2.1.1.228: tRNA (guanine(37)-N(1))-methyltransferase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0008168 methyltransferase activity
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0052906 tRNA (guanine(37)-N1)-methyltransferase activity
Biological Process
GO:0002939 tRNA N1-guanine methylation
GO:0006400 tRNA modification
GO:0008033 tRNA processing
GO:0030488 tRNA methylation
GO:0032259 methylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1p9p, PDBe:1p9p, PDBj:1p9p
PDBsum1p9p
PubMed14583191
UniProtP0A873|TRMD_ECOLI tRNA (guanine-N(1)-)-methyltransferase (Gene Name=trmD)

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