Structure of PDB 5lom Chain A Binding Site BS01

Receptor Information

>5lom Chain A (length=241) Species: 176299 (Agrobacterium fabrum str. C58)

DNPLGLIDPTTISVGTMGDAKPYAFTTADGNFTGFDIELFLNVAGRLGFK
KEQVVFTGQEFSALMPSVANGRFDVAAAAIGTTAKRKETVDFSDGYLAGF
LSVLTSEAGITDAAGLKGKRLGVVQGTLQEIYAEKNFAGTDLVKFPDNNS
AVSALNNGTVDAHFLDFEAAKDYSARYPALKIAVNIPSFDAPAGFVIRKG
NDALRNALDKGLKEAMQDGTWKKLHEKWFPGTPMPAAYLPK

Ligand information

• Ligand ID: SNW
• InChI: InChI=1S/C11H20N2O8/c12-7(15)2-1-5(10(18)19)13-4-11(20)9(17)8(16)6(14)3-21-11/h5-6,8-9,13-14,16-17,20H,1-4H2,(H2,12,15)(H,18,19)/t5-,6+,8+,9-,11+/m0/s1
• InChIKey: SNIATPDKUZZXAT-VISRLPHGSA-N
• SMILES:
  CACTVS 3.385: NC(=O)CC[C@H](NC[C@@]1(O)OC[C@@H](O)[C@@H](O)[C@@H]1O)C(O)=O
  CACTVS 3.385: NC(=O)CC[CH](NC[C]1(O)OC[CH](O)[CH](O)[CH]1O)C(O)=O
  OpenEye OEToolkits 2.0.5: C1[C@H]([C@H]([C@@H]([C@](O1)(CN[C@@H](CCC(=O)N)C(=O)O)O)O)O)O
  OpenEye OEToolkits 2.0.5: C1C(C(C(C(O1)(CNC(CCC(=O)N)C(=O)O)O)O)O)O
• Formula: C11 H20 N2 O8
• Name: Deoxyfructosylglutamine;
  santhopine
• ZINC: ZINC000584905675
• PDB chain: 5lom Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5lom Structural Basis for High Specificity of Amadori Compound and Mannopine Opine Binding in Bacterial Pathogens.
• Resolution: 1.5 Å
• Binding residue (original residue number in PDB): F96 A113 A114 G116 R121 A133 G134 T162 L163 Q164 D201 S223 A226
• Binding residue (residue number reindexed from 1): F61 A78 A79 G81 R86 A98 G99 T127 L128 Q129 D166 S188 A191
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=7.13,Kd=74.1nM

Gene Ontology

Molecular Function

• GO:0015276 ligand-gated monoatomic ion channel activity

Biological Process

• GO:0034220 monoatomic ion transmembrane transport

Cellular Component

• GO:0016020 membrane
• GO:0042597 periplasmic space

External links

• PDB: RCSB:5lom, PDBe:5lom, PDBj:5lom
• PDBsum: 5lom
• PubMed: 27609514
• UniProt: Q7D447