Structure of PDB 3g5s Chain A Binding Site BS01

Receptor Information
>3g5s Chain A (length=424) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MERVNVVGAGLAGSEAAWTLLRLGVPVRLFEMRPKRMTPAHGTDRFAEIV
CSNSLGGEGETNAKGLLQAEMRRAGSLVMEAADLARVPAGGALAVDREEF
SGYITERLTGHPLLEVVREEVREIPPGITVLATGPLTSEALAEALKRRFG
DHFLAYYDAASPIVLYESIDLTKCFRAGRYYLNCPMTEEEYRRFHQALLE
AQRHTPHFEACVPVEELARRGYQTLLFGPMKPVGLVDPRTGKEPFAVVQL
RQEDKAGRMWSLVGFQTGLKWPEQKRLIQMIPGLENAEIVRYGVMHRNTY
LNAPRLLGETLEFREAEGLYAAGVLAGVEGYLESAATGFLAGLNAARKAL
GLPPVAPPEESMLGGLVRYLATANPEGFQPMYANWGLVPPVEGRMGKKEK
RQAMYRRGLEAFSAWLSGLNPPLP
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain3g5s Chain A Residue 444 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3g5s Atomic structure of a folate/FAD-dependent tRNA T54 methyltransferase
Resolution1.05 Å
Binding residue
(original residue number in PDB)		G8 G10 L11 A12 E31 M32 R33 C51 S52 E120 V121 T133 G134 P135 S138 H212 G335 V336 E341 G342 Y343 S346
Binding residue
(residue number reindexed from 1)		G8 G10 L11 A12 E31 M32 R33 C51 S52 E120 V121 T133 G134 P135 S138 H207 G323 V324 E329 G330 Y331 S334
Annotation score2
Enzymatic activity
Enzyme Commision number 2.1.1.74: methylenetetrahydrofolate--tRNA-(uracil(54)-C(5))-methyltransferase [NAD(P)H-oxidizing].
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
GO:0047151 tRNA (uracil(54)-C5)-methyltransferase activity, 5,10-methylenetetrahydrofolate-dependent
GO:0050660 flavin adenine dinucleotide binding
Biological Process
GO:0002098 tRNA wobble uridine modification
GO:0008033 tRNA processing
GO:0030488 tRNA methylation
GO:0032259 methylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3g5s, PDBe:3g5s, PDBj:3g5s
PDBsum3g5s
PubMed19416846
UniProtQ5SID2|TRMFO_THET8 Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO (Gene Name=trmFO)

[Back to BioLiP]