Structure of PDB 8xvd Chain J Binding Site BS01

Receptor Information

>8xvd Chain J (length=235) Species: 2681603 (Escherichia phage Mu)

LPEPPRFVETQTVKQIWTSMRFASLTESIAVVCGNPGVGKTEAAREYRRT
NNNVWMITITPSCASVLECLTELAFELGMNDAPRRKGPLSRALRRRLEGT
QGLVIIDEADHLGAEVLEELRLLQESTRIGLVLMGNHRVYSNMTTVEFAR
LFSRIAKRTAINKTKKADVKAIADAWQINGEKELELLQQIAQKPGALRIL
NHSLRLAAMTAHGKGERVNEDYLRQAFRELDLDVD

Ligand information

• Ligand ID: ADP
• InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 8xvd Chain J Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8xvd Elucidating the Architectural dynamics of MuB filaments in bacteriophage Mu DNA transposition.
• Resolution: 4.43 Å
• Binding residue (original residue number in PDB): F73 V74 P102 G103 V104 G105 K106 T107 E108 L267 R268 N271
• Binding residue (residue number reindexed from 1): F7 V8 P36 G37 V38 G39 K40 T41 E42 L197 R198 N201
• Annotation score: 5

External links

• PDB: RCSB:8xvd, PDBe:8xvd, PDBj:8xvd
• PDBsum: 8xvd
• PubMed: 39085263
• UniProt: P03763|TARGB_BPMU ATP-dependent target DNA activator B (Gene Name=B)