Structure of PDB 5wyr Chain B Binding Site BS02

Receptor Information
>5wyr Chain B (length=248) 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
LVDAVTRLLPGALGHADSAEEDSFTDGLLDCPHYTRPEVYADKRVPEVLL
SGNHEHIRRWRLQQALGRTWERRADLLDSRSLSGEEQKLLAEYIRQRD
Ligand information
Ligand IDSFG
InChIInChI=1S/C15H23N7O5/c16-6(1-2-7(17)15(25)26)3-8-10(23)11(24)14(27-8)22-5-21-9-12(18)19-4-20-13(9)22/h4-8,10-11,14,23-24H,1-3,16-17H2,(H,25,26)(H2,18,19,20)/t6-,7-,8+,10+,11+,14+/m0/s1
InChIKeyLMXOHSDXUQEUSF-YECHIGJVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)C[C@H](CC[C@@H](C(=O)O)N)N)O)O)N
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CC(CCC(C(=O)O)N)N)O)O)N
CACTVS 3.370N[CH](CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.370N[C@@H](CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 12.01O=C(O)C(N)CCC(N)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H23 N7 O5
NameSINEFUNGIN;
ADENOSYL-ORNITHINE
ChEMBLCHEMBL1214186
DrugBankDB01910
ZINCZINC000004217451
PDB chain5wyr Chain B Residue 400 [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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PDB5wyr Crystal structure and catalytic mechanism of the essential m1G37 tRNA methyltransferase TrmD fromPseudomonas aeruginosa.
Resolution2.45 Å
Binding residue
(original residue number in PDB)		Y91 L92 S93 P94 G118 Y120 E121 I138 V142 L143 S144 G145 G146 P149
Binding residue
(residue number reindexed from 1)		Y89 L90 S91 P92 G116 Y118 E119 I136 V140 L141 S142 G143 G144 P147
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=6.39,Kd=0.41uM
Enzymatic activity
Catalytic site (original residue number in PDB) P94 E121 R159 D174
Catalytic site (residue number reindexed from 1) P92 E119 R157 D172
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5wyr, PDBe:5wyr, PDBj:5wyr
PDBsum5wyr
PubMed31399541
UniProtQ02RL6|TRMD_PSEAB tRNA (guanine-N(1)-)-methyltransferase (Gene Name=trmD)

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