Structure of PDB 3pvc Chain A Binding Site BS01

Receptor Information
>3pvc Chain A (length=635) Species: 632 (Yersinia pestis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FSNEDGLEETHHVFLKGNGFPARFASHPQQSCIFAETGFGTGLNFLTLWR
DFALFRQQSPNATLRRLHYISFEKYPLHVADLASAHARWPELASFAEQLR
AQWPLPLAGCHRILLADGAITLDLWFGDVNTLLPTLDDSLNNQVDAWFLD
GFAPNPDMWNEQLFNAMARMTRPGGTFSTFTAAGFVRRGLQQAGFNVTKV
KGFGQKREMLTGTLPQQIHAPTAPWYHRPAATRCDDIAIIGGGIVSALTA
LALQRRGAVVTLYCADAQPAQGASGNRQGALYPLLNGKNDALETFFTSAF
TFARRQYDQLLEQGIAFDHQWCGVSQLAFDDKSRGKIEKMLHTQWPVEFA
EAMSREQLSELAGLDCAHDGIHYPAGGWLCPSDLTHALMMLAQQNGMTCH
YQHELQRLKRIDSQWQLTFGSQAAKHHATVILATGHRLPEWEQTHHLPLS
AVRGQVSHIPTTPVLSQLQQVLCYDGYLTPVNPANQHHCIGASYQRGDIA
TDFRLTEQQENRERLLRCLPQVSWPQQVDVSDNQARCGVRCAIRDHLPMV
GAVPDYAATLAQYQDLSRRINDIAVAPVWPELFMVGGLGSRGLCSAPLVA
EILAAQMFGEPLPLDAKTLAALNPNRFWIRKLLKG
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 chain3pvc 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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PDB3pvc Structural basis for hypermodification of the wobble uridine in tRNA by bifunctional enzyme MnmC.
Resolution2.31 Å
Binding residue
(original residue number in PDB)		I270 G271 G272 G273 I274 V275 A295 D296 A303 S304 N306 A310 E434 L435 T465 R468 G485 V487 Y508 G569 L627 G628 S629 R630 G631 L632
Binding residue
(residue number reindexed from 1)		I240 G241 G242 G243 I244 V245 A265 D266 A273 S274 N276 A280 E404 L405 T434 R437 G454 V456 Y477 G538 L588 G589 S590 R591 G592 L593
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:3pvc, PDBe:3pvc, PDBj:3pvc
PDBsum3pvc
PubMed23617613
UniProtQ8ZD36|MNMC_YERPE tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC (Gene Name=mnmC)

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