Structure of PDB 3sgl Chain A Binding Site BS01

Receptor Information
>3sgl Chain A (length=630) Species: 632 (Yersinia pestis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLEETHHVFLKGNGFPARFASHPQQSCIFAETGFGTGLNFLTLWRDFALF
RQQSPNATLRRLHYISFEKYPLHVADLASAHARWPELASFAEQLRAQWPL
PLAGCHRILLADGAITLDLWFGDVNTLLPTLDDSLNNQVDAWFLDGFAPA
KNPDMWNEQLFNAMARMTRPGGTFSTFTAAGFVRRGLQQAGFNVTKVKGF
GQKREMLTGTLPQQIHAPTAPWYHRPAATRCDDIAIIGGGIVSALTALAL
QRRGAVVTLYCADAQPAQGASGNRQGALYPLLNGKNDALETFFTSAFTFA
RRQYDQLLEQGIAFDHQWCGVSQLAFDDKSRGKIEKMLHTQWPVEFAEAM
SREQLSELAGLDCAHDGIHYPAGGWLCPSDLTHALMMLAQQNGMTCHYQH
ELQRLKRIDSQWQLTFGQAAKHHATVILATGHRLPEWEQTHHLPLSAVRG
QVSHIPTTPVLSQLQQVLCYDGYLTPVNPANQHHCIGASYQRGDIATDFR
LTEQQENRERLLRCLPQVSWPQQVDVSDNQARCGVRCAIRDHLPMVGAVP
DYAATLAQYQDLSRRIDIAVAPVWPELFMVGGLGSRGLCSAPLVAEILAA
QMFGEPLPLDAKTLAALNPNRFWIRKLLKG
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 chain3sgl Chain A Residue 690 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3sgl Structural basis for hypermodification of the wobble uridine in tRNA by bifunctional enzyme MnmC.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		I270 G271 G272 G273 I274 V275 A295 D296 A303 S304 N306 A310 E434 L435 T465 G485 Y508 G569 L627 G628 S629 R630 G631 L632
Binding residue
(residue number reindexed from 1)		I237 G238 G239 G240 I241 V242 A262 D263 A270 S271 N273 A277 E401 L402 T430 G450 Y473 G534 L583 G584 S585 R586 G587 L588
Annotation score1
Enzymatic activity
Enzyme Commision number 1.5.-.-
2.1.1.61: tRNA 5-(aminomethyl)-2-thiouridylate-methyltransferase.
Gene Ontology
Molecular Function
GO:0004808 tRNA (5-methylaminomethyl-2-thiouridylate)(34)-methyltransferase activity
GO:0008168 methyltransferase activity
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity
GO:0016491 oxidoreductase activity
GO:0016645 oxidoreductase activity, acting on the CH-NH group of donors
GO:0050660 flavin adenine dinucleotide binding
Biological Process
GO:0002097 tRNA wobble base modification
GO:0002098 tRNA wobble uridine modification
GO:0008033 tRNA processing
GO:0032259 methylation
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3sgl, PDBe:3sgl, PDBj:3sgl
PDBsum3sgl
PubMed23617613
UniProtQ8ZD36|MNMC_YERPE tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC (Gene Name=mnmC)

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