Structure of PDB 2vp3 Chain A Binding Site BS02

Receptor Information
>2vp3 Chain A (length=291) Species: 10254 (Vaccinia virus WR) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDVVSLDKPFMYFEEIDNELDYEPESANEVAKKLPYQGQLKLLLGELFFL
SKLQRHGILDGATVVYIGSAPGTHIRYLRDHFYNLGVIIKWMLIDGRHHD
PILNGLRDVTLVTRFVDEEYLRSIKKQLHPSKIILISDVRSPSTADLLSN
YALQNVMISILNPVASSLKWRCPFPDQWIKDFYIPHGNKMLQPFAPSYSA
EMRLLSIYTGENMRLTRVTKSDAVNYEKKMYYLNKIVRNKVVVNFDYPNQ
EYDYFHMYFMLRTVYCNKTFPTTKAKVLFLQQSIFRFLNIP
Ligand information
Ligand IDM7G
InChIInChI=1S/C11H17N5O11P2/c1-15-3-16(8-5(15)9(19)14-11(12)13-8)10-7(18)6(17)4(26-10)2-25-29(23,24)27-28(20,21)22/h3-4,6-7,10,17-18H,2H2,1H3,(H5-,12,13,14,19,20,21,22,23,24)/p+1/t4-,6-,7-,10-/m1/s1
InChIKeySBASPRRECYVBRF-KQYNXXCUSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7C[n+]1cn(c2c1C(=O)NC(=N2)N)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC1OC(n2c[n+](C)c3c2N=C(N)NC3=O)C(O)C1O
OpenEye OEToolkits 2.0.7C[n+]1cn(c2c1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.385C[n+]1cn([CH]2O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O)c3N=C(N)NC(=O)c13
CACTVS 3.385C[n+]1cn([C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O)c3N=C(N)NC(=O)c13
FormulaC11 H18 N5 O11 P2
Name7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE
ChEMBL
DrugBankDB01960
ZINCZINC000013548083
PDB chain2vp3 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

[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]
PDB2vp3 Specific protein recognition of an mRNA cap through its alkylated base.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		Y22 A27 P148 R177 F180 D182 E233
Binding residue
(residue number reindexed from 1)		Y22 A27 P142 R171 F174 D176 E227
Annotation score1
Enzymatic activity
Enzyme Commision number 2.1.1.57: methyltransferase cap1.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003746 translation elongation factor activity
GO:0004483 mRNA (nucleoside-2'-O-)-methyltransferase activity
GO:0008168 methyltransferase activity
Biological Process
GO:0006370 7-methylguanosine mRNA capping
GO:0006412 translation
GO:0006414 translational elongation
GO:0031440 regulation of mRNA 3'-end processing
GO:0032259 methylation
Cellular Component
GO:0044423 virion component

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2vp3, PDBe:2vp3, PDBj:2vp3
PDBsum2vp3
PubMed9145102
UniProtP07617|MCE_VACCW Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase (Gene Name=OPG102)

[Back to BioLiP]