Structure of PDB 6sa0 Chain D Binding Site BS04

Receptor Information

>6sa0 Chain D (length=333) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

SAATELDVDGVKVRFTNPDKVYFPKLGKNGTKGKLVEYYLSVASGPMLAL
LRDRPVHLQRFPDGIEGEEIYQKRVPQKHPDYLETCVVTFPSGRTADALK
ITHPSSIIWAAQMGTVTLHPWQVRCPDTEHPDELRVDLDPQPGTGFKEAR
TVACDVLKPLLDELGLVGYPKTSGGRGVHVFLRIKPQWDFIEVRRAGIAL
AREVERRAPDAVTTSWWKEERGERLFIDYNQNARDRTFASAYSVRKTPIA
TVSMPLSWDELRNADPDDYTMNTVPDLLAGRDDPWADIDSVQQSLGPLLD
LVAADEERGLGDLPYPPNYPKMPGEPPRVQPSK

Ligand information

• Ligand ID: 2KH
• InChI: InChI=1S/C9H16N3O14P3/c13-5-1-2-12(9(16)10-5)8-7(15)6(14)4(25-8)3-24-27(17,18)11-28(19,20)26-29(21,22)23/h1-2,4,6-8,14-15H,3H2,(H,10,13,16)(H2,21,22,23)(H3,11,17,18,19,20)/t4-,6-,7-,8-/m1/s1
• InChIKey: OZIBFYOFLVBDIY-XVFCMESISA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)O
  ACDLabs 12.01: O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
  CACTVS 3.385: O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
  CACTVS 3.385: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
  OpenEye OEToolkits 1.7.6: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)O
• Formula: C9 H16 N3 O14 P3
• Name: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine
• ZINC: ZINC000098208190
• PDB chain: 6sa0 Chain D Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6sa0 Molecular basis for DNA repair synthesis on short gaps by mycobacterial Primase-Polymerase C.
• Resolution: 2.209 Å
• Binding residue (original residue number in PDB): Y74 H122 D140 D142 S176 R179 G180 H182 Q234 T240 F241 A242 R248
• Binding residue (residue number reindexed from 1): Y71 H119 D137 D139 S173 R176 G177 H179 Q231 T237 F238 A239 R245
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0046872 metal ion binding

External links

• PDB: RCSB:6sa0, PDBe:6sa0, PDBj:6sa0
• PDBsum: 6sa0
• PubMed: 32826907
• UniProt: A0R5T1