Structure of PDB 3b89 Chain A Binding Site BS01

Receptor Information

>3b89 Chain A (length=240) Species: 562 (Escherichia coli)

NINDALTSILASKKYRALCPDTVRRILTEEWGRHKSPKQTVEAARTRLHG
ICGAVTPESLKAAAAALSAGDVKKALSLHASTKERLAELDTLYDFIFSAE
TPRRVLDIACGLNPLALYERGIASVWGCDIHQGLGDVITPFAREKDWDFT
FALQDVLCAPPAEAGDLALIFKLLPLLEREQAGSAMALLQSLNTPRMAVS
FPTRSEANYAAWFEGGLPAEFEIEDKKTIGTELIYLIKKN

Ligand information

• Ligand ID: 5GP
• InChI: InChI=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
• InChIKey: RQFCJASXJCIDSX-UUOKFMHZSA-N
• SMILES:
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3O)COP(=O)(O)O
  OpenEye OEToolkits 1.5.0: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
  OpenEye OEToolkits 1.5.0: c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
• Formula: C10 H14 N5 O8 P
• Name: GUANOSINE-5'-MONOPHOSPHATE
• ChEMBL: CHEMBL283807
• DrugBank: DB01972
• ZINC: ZINC000002159505
• PDB chain: 3b89 Chain A Residue 500

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3b89 Crystal structure of rRNA methylase from Escherichia coli.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): S83 A111 D131 I132 Q156 D157 V158
• Binding residue (residue number reindexed from 1): S81 A109 D129 I130 Q154 D155 V156
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.1.1.179: 16S rRNA (guanine(1405)-N(7))-methyltransferase.

Gene Ontology

Molecular Function

• GO:0008168 methyltransferase activity
• GO:0008649 rRNA methyltransferase activity

Biological Process

• GO:0006364 rRNA processing
• GO:0031167 rRNA methylation
• GO:0032259 methylation
• GO:0046677 response to antibiotic

External links

• PDB: RCSB:3b89, PDBe:3b89, PDBj:3b89
• PDBsum: 3b89
• UniProt: Q763K9