Structure of PDB 5idm Chain A Binding Site BS01

Receptor Information

>5idm Chain A (length=177) Species: 155892 (Caulobacter vibrioides)

VQREVLDLGELISEFEVLLRRLLREDVKLITDYGRDLPQVRADKSQLETA
VMNLAVNARDAVRAAKGGGVVRIRTARLTRDEAIQLGFPAADGDTAFIEV
SDDGPGIPPDVMGKIFDPFFTTKPVGEGTGLGLATVYGIVKQSDGWIHVH
SRPNEGAAFRIFLPVYEAPAALEHHHH

Ligand information

• Ligand ID: ANP
• InChI: InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
• InChIKey: PVKSNHVPLWYQGJ-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
  CACTVS 3.370: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
  CACTVS 3.370: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
  ACDLabs 12.01: O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.7.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
• Formula: C10 H17 N6 O12 P3
• Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
• ChEMBL: CHEMBL1230989
• ZINC: ZINC000008660410
• PDB chain: 5idm Chain A Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5idm Cyclic di-GMP mediates a histidine kinase/phosphatase switch by noncovalent domain cross-linking.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): N434 A438 I484 T498 T499 K500 T506 G507 G509 L510 F536
• Binding residue (residue number reindexed from 1): N57 A61 I107 T121 T122 K123 T129 G130 G132 L133 F159
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 2.7.13.3: histidine kinase.

Gene Ontology

Molecular Function

• GO:0016772 transferase activity, transferring phosphorus-containing groups

Biological Process

• GO:0016310 phosphorylation

External links

• PDB: RCSB:5idm, PDBe:5idm, PDBj:5idm
• PDBsum: 5idm
• PubMed: 27652341
• UniProt: Q9X688