Structure of PDB 3mct Chain A Binding Site BS02

Receptor Information

>3mct Chain A (length=291) Species: 10245 (Vaccinia virus)

MDVVSLDKPFMYFEEIDNELDYEPESANEVAKKLPYQGQLKLLLGELFFL
SKLQRHGILDGATVVYIGSAPGTHIRYLRDHFYNLGVIIKWMLIDGRHHD
PILNGLRDVTLVTRFVDEEYLRSIKKQLHPSKIILISDVRSPSTADLLSN
YALQNVMISILNPVASSLKWRCPFPDQWIKDFYIPHGNKMLQPFAPSYSA
EMRLLSIYTGENMRLTRVTKSDAVNYEKKMYYLNKIVRNKVVVNFDYPNQ
EYDYFHMYFMLRTVYCNKTFPTTKAKVLFLQQSIFRFLNIP

Ligand information

• Ligand ID: 3MC
• InChI: InChI=1S/C5H7N3O/c1-8-4(6)2-3-7-5(8)9/h2-3H,1H3,(H2,6,7,9)/p+1
• InChIKey: UPHQQDZIRIHPHU-UHFFFAOYSA-O
• SMILES:
  OpenEye OEToolkits 1.5.0: C[N+]1=C(C=CNC1=O)N
  ACDLabs 10.04: O=C1[N+](=C(N)C=CN1)C
  CACTVS 3.341: C[N+]1=C(N)C=CNC1=O
• Formula: C5 H8 N3 O
• Name: 3-METHYLCYTOSINE
• DrugBank: DB04103
• ZINC: ZINC000100033918
• PDB chain: 3mct Chain A Residue 600

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3mct mRNA cap recognition: dominant role of enhanced stacking interactions between methylated bases and protein aromatic side chains.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): Y22 F180 E233
• Binding residue (residue number reindexed from 1): Y22 F174 E227
• Annotation score: 1
• Binding affinity: MOAD: Kd=85.5uM
  PDBbind-CN: -logKd/Ki=4.07,Kd=85.5uM

Enzymatic activity

• Enzyme Commision number: 2.1.1.57: methyltransferase cap1.

Gene Ontology

Molecular Function

• GO:0003746 translation elongation factor activity
• GO:0004483 mRNA (nucleoside-2'-O-)-methyltransferase activity

Biological Process

• GO:0006370 7-methylguanosine mRNA capping
• GO:0031440 regulation of mRNA 3'-end processing

External links

• PDB: RCSB:3mct, PDBe:3mct, PDBj:3mct
• PDBsum: 3mct
• PubMed: 10377383
• UniProt: P07617|MCE_VACCW Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase (Gene Name=OPG102)