Structure of PDB 5l9g Chain A Binding Site BS01

Receptor Information

>5l9g Chain A (length=325) Species: 1183423 (Agrobacterium tumefaciens str. B6)

MDVVIASSGGGWQEAQDKALWAPAAKALNITYTQDTFQNWAEARAQVESG
SVTWDIIQIGIADEPQAKAAGVLEKLDPDIVNKADFPPGSVTDSFVANSN
YSTLIAWNKKTYGDNGPKSMADFFDVKKFPGKRALWNQPIGMIEAAALAL
GTPRDKVYEFLSTEEGRKAAIAKLTELAPSVSVWWESGAQAAQLIKDGEV
DMIITWGGRVQGAINDGANFAYTFNDAQLGTDGYAIVKGAPHRDAAMRFL
KEMSKAEYQKDLPNSFATAPANMKAYDLAKYTPEKMATMASAPENVAVQY
SVDPNFWAKHAKWASEAYDNVRLSR

Ligand information

• Ligand ID: MO0
• InChI: InChI=1S/C11H22N2O8/c12-8(17)2-1-5(11(20)21)13-3-6(15)9(18)10(19)7(16)4-14/h5-7,9-10,13-16,18-19H,1-4H2,(H2,12,17)(H,20,21)/t5-,6+,7+,9+,10+/m0/s1
• InChIKey: VPRLICVDSGMIKO-SZWOQXJISA-N
• SMILES:
  CACTVS 3.385: NC(=O)CC[CH](NC[CH](O)[CH](O)[CH](O)[CH](O)CO)C(O)=O
  OpenEye OEToolkits 2.0.5: C(CC(=O)N)[C@@H](C(=O)O)NC[C@H]([C@H]([C@@H]([C@@H](CO)O)O)O)O
  OpenEye OEToolkits 2.0.5: C(CC(=O)N)C(C(=O)O)NCC(C(C(C(CO)O)O)O)O
  CACTVS 3.385: NC(=O)CC[C@H](NC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO)C(O)=O
• Formula: C11 H22 N2 O8
• Name: mannopine
• ZINC: ZINC000005112885
• PDB chain: 5l9g Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5l9g Structural Basis for High Specificity of Amadori Compound and Mannopine Opine Binding in Bacterial Pathogens.
• Resolution: 1.75 Å
• Binding residue (original residue number in PDB): W41 Q67 Q87 I88 G89 D92 Y130 W235 R238 D261 T297
• Binding residue (residue number reindexed from 1): W12 Q38 Q58 I59 G60 D63 Y101 W206 R209 D232 T268
• Annotation score: 1
• Binding affinity: MOAD: Kd=19.8nM
  PDBbind-CN: -logKd/Ki=7.70,Kd=19.8nM

External links

• PDB: RCSB:5l9g, PDBe:5l9g, PDBj:5l9g
• PDBsum: 5l9g
• PubMed: 27609514