Structure of PDB 6sa1 Chain A Binding Site BS05

Receptor Information

>6sa1 Chain A (length=328) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

SAATELDVDGVKVRFTNPDKVYFPKLGKNGTKGKLVEYYLSVASGPMLAL
LRDRPVHLQRFPDGIEGEEIYQKRVPQKHPDYLETCVVTFPSGRTADALK
ITHPSSIIWAAQMGTVTLHPWQVRCPDTEHPDELRVDLDPQPGTGFKEAR
TVACDVLKPLLDELGLVGYPKTSGGRGVHVFLRIKPQWDFIEVRRAGIAL
AREVERRAPDAVTTSWWKEERGERLFIDYNQNARDRTFASAYSVRKTPIA
TVSMPLSWDELRNADPDDYTMNTVPDLLAGRDDPWADIDSVQQSLGPLLD
LVAADEERGLGDLPYPPNYPKMPGEPPR

Ligand information

• Ligand ID: U3H
• InChI: InChI=1S/C9H17N2O14P3/c12-6-3-5(23-8(6)11-2-1-7(13)10-9(11)14)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8-9,12,14H,3-4H2,(H,10,13)(H,18,19)(H,20,21)(H2,15,16,17)/t5-,6+,8+,9+/m0/s1
• InChIKey: CVEDUOUYNXHQBA-HIORRCEOSA-N
• SMILES:
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C=CC(=O)NC1O)C(O)C2
  CACTVS 3.341: O[C@@H]1C[C@@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)O[C@H]1N2C=CC(=O)N[C@H]2O
  OpenEye OEToolkits 1.5.0: C1C(OC(C1O)N2C=CC(=O)NC2O)COP(=O)(O)OP(=O)(O)OP(=O)(O)O
  CACTVS 3.341: O[CH]1C[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O[CH]1N2C=CC(=O)N[CH]2O
  OpenEye OEToolkits 1.5.0: C1[C@H](O[C@H]([C@@H]1O)N2C=CC(=O)NC2O)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O
• Formula: C9 H17 N2 O14 P3
• Name: 3'-DEOXY-URIDINE 5'-TRIPHOSPHATE
• ZINC: ZINC000033821547
• PDB chain: 6sa1 Chain A Residue 403

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6sa1 Molecular basis for DNA repair synthesis on short gaps by mycobacterial Primase-Polymerase C.
• Resolution: 2.01 Å
• Binding residue (original residue number in PDB): H122 D142 S176 G178 R179 G180 Q234 R239 T240 F241 R248
• Binding residue (residue number reindexed from 1): H119 D139 S173 G175 R176 G177 Q231 R236 T237 F238 R245
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0046872 metal ion binding

External links

• PDB: RCSB:6sa1, PDBe:6sa1, PDBj:6sa1
• PDBsum: 6sa1
• PubMed: 32826907
• UniProt: A0R5T1