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Structure of PDB 3gcm Chain A Binding Site BS04

Receptor Information
>3gcm Chain A (length=544) Species: 331111 (Escherichia coli O139:H28 str. E24377A) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAK
PGQDFFPLTVNYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRP
LFPEGFVNEVQVIATVVSVNPQVNPDIVAMIGASAALSLSGIPFNGPIGA
ARVGYINDQYVLNPTQDELKESKLDLVVAGTEAAVLMVESEAELLSEDQM
LGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVNEALNARVAALAE
ARLSDAYRITDKQERYAQVDVIKSETIATLLAEDETLDENELGEILHAIE
KNVVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQAL
VTATLGTARDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREI
GHGRLAKRGVLAVMPDMDKFPYTVRVVSEITESNGSSSMASVCGASLALM
DAGVPIKAAVAGIAMGLVKEGDNYVVLSDILGDEDHLGDMDFKVAGSRDG
ISALQMDIKIEGITKEIMQVALNQAKGARLHILGVMEQAINAPR
Ligand information
Ligand ID5GP
InChIInChI=1S/C10H14N5O8P/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(23-9)1-22-24(19,20)21/h2-3,5-6,9,16-17H,1H2,(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyRQFCJASXJCIDSX-UUOKFMHZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3O)COP(=O)(O)O
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H14 N5 O8 P
NameGUANOSINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL283807
DrugBankDB01972
ZINCZINC000002159505
PDB chain3gcm Chain C Residue 550 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3gcm Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		F77 F78
Binding residue
(residue number reindexed from 1)		F76 F77
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.8: polyribonucleotide nucleotidyltransferase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0004654 polyribonucleotide nucleotidyltransferase activity
Biological Process
GO:0006396 RNA processing
GO:0006402 mRNA catabolic process

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:3gcm, PDBe:3gcm, PDBj:3gcm
PDBsum3gcm
PubMed19327365
UniProtA7ZS61|PNP_ECO24 Polyribonucleotide nucleotidyltransferase (Gene Name=pnp)

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