Structure of PDB 5wyq Chain B Binding Site BS01

Receptor Information
>5wyq Chain B (length=240) Species: 208963 (Pseudomonas aeruginosa UCBPP-PA14) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMLWVGVVSIFPEMFRAISDYGITSRAVKQGLLTLTCWNPRVYTEDRHQT
VDDRPFGGGPGMVMKIKPLEGALADARQAAGGRKAKVIYLSPQGRQLTQA
GVRELAEEEALILIAGRYEGIDERFIEEHVDEEWSIGDYVLSGGELPAMV
LVDAVTRLLPGALDSFTDGLLDCPHYTRPEVYADKRVPEVLLSGNHEHIR
RWRLQQALGRTWERRADLLDSRSLSGEEQKLLAEYIRQRD
Ligand information
Ligand IDSAM
InChIInChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
InChIKeyMEFKEPWMEQBLKI-FCKMPRQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
ACDLabs 10.04[O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H22 N6 O5 S
NameS-ADENOSYLMETHIONINE
ChEMBLCHEMBL1235831
DrugBank
ZINC
PDB chain5wyq Chain A Residue 401 [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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PDB5wyq Crystal structure and catalytic mechanism of the essential m1G37 tRNA methyltransferase TrmD fromPseudomonas aeruginosa.
Resolution2.16 Å
Binding residue
(original residue number in PDB)		D182 H185
Binding residue
(residue number reindexed from 1)		D172 H175
Annotation score5
Binding affinityPDBbind-CN: -logKd/Ki=4.84,Kd=14.4uM
Enzymatic activity
Catalytic site (original residue number in PDB) P94 E121 R159 D174
Catalytic site (residue number reindexed from 1) P92 E119 R157 D164
Enzyme Commision number 2.1.1.228: tRNA (guanine(37)-N(1))-methyltransferase.
Gene Ontology
Molecular Function
GO:0008168 methyltransferase 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:0032259 methylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5wyq, PDBe:5wyq, PDBj:5wyq
PDBsum5wyq
PubMed31399541
UniProtQ02RL6|TRMD_PSEAB tRNA (guanine-N(1)-)-methyltransferase (Gene Name=trmD)

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