Structure of PDB 1d6a Chain A Binding Site BS01

Receptor Information
>1d6a Chain A (length=262) Species: 3527 (Phytolacca americana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VNTIIYNVGSTTISKYATFLNDLRNEAKDPSLKCYGIPMLPNTNTNPKYV
LVELQGSNKKTITLMLRRNNLYVMGYSDPFETNKCRYHIFNDISGTERQD
VETTLCPNANSRVSKNINFDSRYPTLESKAGVKSRSQVQLGIQILDSNIG
KISGVMSFTEKTEAEFLLVAIQMVSEAARFKYIENQVKTNFNRAFNPNPK
VLNLQETWGKISTAIHDAKNGVLPKPLELVDASGAKWIVLRVDEIKPDVA
LLNYVGGSCQTT
Ligand information
Ligand IDGUN
InChIInChI=1S/C5H5N5O/c6-5-9-3-2(4(11)10-5)7-1-8-3/h1H,(H4,6,7,8,9,10,11)
InChIKeyUYTPUPDQBNUYGX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=Nc2[nH]cnc2C(=O)N1
ACDLabs 10.04O=C1c2ncnc2N=C(N1)N
OpenEye OEToolkits 1.5.0c1[nH]c2c(n1)C(=O)NC(=N2)N
FormulaC5 H5 N5 O
NameGUANINE
ChEMBLCHEMBL219568
DrugBankDB02377
ZINCZINC000000895129
PDB chain1d6a Chain A Residue 901 [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]
PDB1d6a X-ray crystallographic analysis of the structural basis for the interaction of pokeweed antiviral protein with guanine residues of ribosomal RNA.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		Y72 V73 S121 Y123 I171 R179
Binding residue
(residue number reindexed from 1)		Y72 V73 S121 Y123 I171 R179
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) V73 E176 R179
Catalytic site (residue number reindexed from 1) V73 E176 R179
Enzyme Commision number 3.2.2.22: rRNA N-glycosylase.
Gene Ontology
Molecular Function
GO:0016787 hydrolase activity
GO:0030598 rRNA N-glycosylase activity
GO:0090729 toxin activity
Biological Process
GO:0017148 negative regulation of translation
GO:0035821 modulation of process of another organism
GO:0051607 defense response to virus

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1d6a, PDBe:1d6a, PDBj:1d6a
PDBsum1d6a
PubMed10595542
UniProtP10297|RIP1_PHYAM Antiviral protein I (Gene Name=PAP1)

[Back to BioLiP]