Structure of PDB 2far Chain B Binding Site BS03

Receptor Information

>2far Chain B (length=295) Species: 287 (Pseudomonas aeruginosa)

RAATAGVRISHPQRLIDPSIQASKLELAEFHARYADLLLRDLRERPVSLV
RGPDGIGGELFFQKHAARLKIPGIVQLDPALDPGHPPLLQIRSAEALVGA
VQMGSIEFHTWNASLANLERPDRFVLDLDPDPALPWKRMLEATQLSLTLL
DELGLRAFLKTSGGKGMHLLVPLERRHGWDEVKDFAQAISQHLARLMPER
FSAVSGPRNRVGKIFVDYLRNSRGASTVAAYSVRAREGLPVSVPVFREEL
DSLQGANQWNLRSLPQRLDELAGDDPWADYAGTRQRISAAMRRQL

Ligand information

• Ligand ID: DTP
• InChI: InChI=1S/C10H16N5O12P3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(25-7)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H,22,23)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
• InChIKey: SUYVUBYJARFZHO-RRKCRQDMSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O3
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
• Formula: C10 H16 N5 O12 P3
• Name: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
• ChEMBL: CHEMBL335538
• DrugBank: DB03222
• ZINC: ZINC000008215662
• PDB chain: 2far Chain B Residue 1302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2far Atomic structure and nonhomologous end-joining function of the polymerase component of bacterial DNA ligase D
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): D669 S704 K707 H710 R762 R776 R778
• Binding residue (residue number reindexed from 1): D127 S162 K165 H168 R220 R234 R236
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 6.5.1.1: DNA ligase (ATP).

External links

• PDB: RCSB:2far, PDBe:2far, PDBj:2far
• PDBsum: 2far
• PubMed: 16446439
• UniProt: Q9I1X7|LIGD_PSEAE Multifunctional non-homologous end joining protein LigD (Gene Name=ligD)