Structure of PDB 1xm5 Chain D Binding Site BS01

Receptor Information

>1xm5 Chain D (length=152) Species: 562 (Escherichia coli)

MSQVILDLQLACEDNSGLPEESQFQTWLNAVIPQFQEESEVTIRVVDTAE
SHSLNLTYRGKDKPTNVLSFPFEVPPGMEMSLLGDLVICRQVVEKEAQEQ
GKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEALETEIMLALGYEDPY
IA

Ligand information

• Ligand ID: NI
• InChI: InChI=1S/Ni/q+2
• InChIKey: VEQPNABPJHWNSG-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Ni++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Ni+2]
• Formula: Ni
• Name: NICKEL (II) ION
• DrugBank: DB14204
• PDB chain: 1xm5 Chain D Residue 5004

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1xm5 The ybeY protein from Escherichia coli is a metalloprotein.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): H4114 H4118 H4124
• Binding residue (residue number reindexed from 1): H114 H118 H124
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 3.1.-.-

Gene Ontology

Molecular Function

• GO:0004222 metalloendopeptidase activity
• GO:0004519 endonuclease activity
• GO:0004521 RNA endonuclease activity
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0016151 nickel cation binding
• GO:0016892 RNA endonuclease activity, producing 3'-phosphomonoesters
• GO:0046872 metal ion binding

Biological Process

• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0009408 response to heat
• GO:0030490 maturation of SSU-rRNA
• GO:0031564 transcription antitermination
• GO:0042254 ribosome biogenesis
• GO:0042274 ribosomal small subunit biogenesis

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:1xm5, PDBe:1xm5, PDBj:1xm5
• PDBsum: 1xm5
• PubMed: 16511207
• UniProt: P0A898|YBEY_ECOLI Endoribonuclease YbeY (Gene Name=ybeY)