Structure of PDB 7pd3 Chain 4 Binding Site BS03

Receptor Information

>7pd3 Chain 4 (length=37) Species: 9606 (Homo sapiens)

FKNKTVLKKRCKDCYLVKRRGRWYVYCKTHPRHKQRQ

Ligand information

• Ligand ID: U
• InChI: InChI=1S/C9H13N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
• InChIKey: DJJCXFVJDGTHFX-XVFCMESISA-N
• SMILES:
  ACDLabs 10.04: O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)COP(=O)(O)O
  CACTVS 3.341: O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O
  CACTVS 3.341: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
• Formula: C9 H13 N2 O9 P
• Name: URIDINE-5'-MONOPHOSPHATE
• ChEMBL: CHEMBL214393
• DrugBank: DB03685
• ZINC: ZINC000002123545
• PDB chain: 7pd3 Chain 4 Residue 202

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7pd3 Visualizing formation of the active site in the mitochondrial ribosome.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): F66 R85 R101
• Binding residue (residue number reindexed from 1): F1 R20 R36
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0006412 translation
• GO:0032543 mitochondrial translation

Cellular Component

• GO:0005739 mitochondrion
• GO:0005743 mitochondrial inner membrane
• GO:0005762 mitochondrial large ribosomal subunit
• GO:0005840 ribosome
• GO:0016604 nuclear body
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7pd3, PDBe:7pd3, PDBj:7pd3
• PDBsum: 7pd3
• PubMed: 34609277
• UniProt: Q9P0J6|RM36_HUMAN Large ribosomal subunit protein bL36m (Gene Name=MRPL36)