Structure of PDB 2ix0 Chain A Binding Site BS01

Receptor Information
>2ix0 Chain A (length=637) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DDPLLAQLKQQLHSQTPRAEGVVKATEFGFLEVDAQKSYFIPPPQMKKVM
HGDRIIAVIHSERESAEPEELVEPFLTRFVGKVQGKNDRLAIVPDHPLLK
DAIPCRAARGLNHEFKEGDWAVAEMRRHPLKGDRSFYAELTQYITFGDDH
FVPWWVTLARHNLEKEAPDGVATEMLDEGLVREDLTALDFVTIDSASTED
MDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDKAAKIRAFTNYLPGF
NIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEDNIEFFAATIES
KAKLVYDQVSDWLENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNHALV
FKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEEAMIAANICAARVLRDK
LGFGIYNVHMGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELD
AQPTGFLDSRIRRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMIN
HRLLKAVIKGETATRPQDEITVQMAERRRLNRMAERDVGDWLYARFLKDK
AGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQEN
GTVQIKGETVYKVTDVIDVTIAEVRMETRSIIARPVA
Ligand information
Ligand IDC5P
InChIInChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyIERHLVCPSMICTF-XVFCMESISA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
ACDLabs 10.04O=C1N=C(N)C=CN1C2OC(C(O)C2O)COP(=O)(O)O
FormulaC9 H14 N3 O8 P
NameCYTIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL307679
DrugBankDB03403
ZINCZINC000003861744
PDB chain2ix0 Chain A Residue 1645 [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]
PDB2ix0 Unravelling the Dynamics of RNA Degradation by Ribonuclease II and its RNA-Bound Complex
Resolution2.44 Å
Binding residue
(original residue number in PDB)		F82 F86 D102 H103 R167
Binding residue
(residue number reindexed from 1)		F75 F79 D95 H96 R160
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D201 D207 D209 D210 Y313 R500
Catalytic site (residue number reindexed from 1) D194 D200 D202 D203 Y306 R493
Enzyme Commision number 3.1.13.1: exoribonuclease II.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0004527 exonuclease activity
GO:0004540 RNA nuclease activity
GO:0005515 protein binding
GO:0008408 3'-5' exonuclease activity
GO:0008859 exoribonuclease II activity
Biological Process
GO:0006401 RNA catabolic process
GO:0006402 mRNA catabolic process
GO:0016070 RNA metabolic process
GO:0016078 tRNA decay
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2ix0, PDBe:2ix0, PDBj:2ix0
PDBsum2ix0
PubMed16957732
UniProtP30850|RNB_ECOLI Exoribonuclease 2 (Gene Name=rnb)

[Back to BioLiP]