Structure of PDB 6k6w Chain D Binding Site BS01

Receptor Information

>6k6w Chain D (length=443) Species: 176280 (Staphylococcus epidermidis ATCC 12228)

LIKKKNKDIRIIPLGGVGEIAKNMYIVEVDDEMFMLDAGLMFPEDEMLGV
DIVIPDIQYVIENKERLKGIFLTHGHEHAIGAVSYVLEQIDAPVYGSKLT
IALVKEAMKARNIKKKVRYYTVNHDSIMRFKNVNVSFFNTTHSIPDSLGV
CIHTSYGSIVYTGEFKFDQSLHGHYAPDLKRMAEIGDEGVFALISDSTEA
EKPGYNTPENIIEHHMYDAFAKVKGRLIVSCYASNFVRIQQVLNIASQLN
RKVSFLGRSLESSFNIARKMGYFDIPKDLLIPINEVENYPKNEVIIIATG
MQGEPVEALSQMARKKHKIMNIEEGDSIFLAITASANMEVIIADTLNELV
RAGAHIIPNNKKIHASSHGCMEELKMMLNIMKPEYFVPVQGEFKMQIAHA
KLAAETGVAPEKIFLVEKGDVISYNGKDMILNEKVQSGNILID

Ligand information

• Ligand ID: MN
• InChI: InChI=1S/Mn/q+2
• InChIKey: WAEMQWOKJMHJLA-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mn+2]
  CACTVS 3.341: [Mn++]
• Formula: Mn
• Name: MANGANESE (II) ION
• DrugBank: DB06757
• PDB chain: 6k6w Chain D Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6k6w Structure of RNase J1 from Staphylococcus epidermidis
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): H76 H78 H80 H144 E166
• Binding residue (residue number reindexed from 1): H74 H76 H78 H142 E164
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 3.1.-.-

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0004519 endonuclease activity
• GO:0004521 RNA endonuclease activity
• GO:0004527 exonuclease activity
• GO:0004534 5'-3' RNA exonuclease activity
• GO:0008270 zinc ion binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006364 rRNA processing
• GO:0006396 RNA processing

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:6k6w, PDBe:6k6w, PDBj:6k6w
• PDBsum: 6k6w
• UniProt: Q8CST0|RNJ2_STAES Ribonuclease J 2 (Gene Name=rnj2)