Structure of PDB 5dvi Chain B Binding Site BS01

Receptor Information

>5dvi Chain B (length=396) Species: 1005395 (Pseudomonas bharatica CSV86)

NPGTVDVLHWWTSGGEAKAVETLKQQIQKDGFIWKDNAVAGGGGAAAMTV
LKTRAISGNPPSAAQIKGPDIQEWGALGLLTELDDVAAANKWDDLLPRQV
ADIMKYDGHYVAVPVNIHRVNWLWINPQVFDKAGAKVPTTLDELFAAADK
LKAAGFIPLAHGGQPWQDSTVFEDLVLSILGPKGYHAAFVDLDEKTLTGP
QMTEAFATLKRLGTYMDPNRAGRDWNIAAAEVINGKAGMQIMGDWAKSEW
SAAGKVAGKDYQCVAFPGTQGSFAYNIDSLAMFKLKDANDIKAQNDLAKV
ALEPEFQTVFNQNKGSLPVRQDMDMSKFDACTQKSAADFKEAAKGDGLQP
SMAHNMATTLAVQGAIFDVVTNFLNDPQAEPATAVKQLNAAIKAAR

Ligand information

• Ligand ID: BGC
• InChI: InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6-/m1/s1
• InChIKey: WQZGKKKJIJFFOK-VFUOTHLCSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: C(C1C(C(C(C(O1)O)O)O)O)O
  CACTVS 3.370: OC[C@H]1O[C@@H](O)[C@H](O)[C@@H](O)[C@@H]1O
  CACTVS 3.370: OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
  OpenEye OEToolkits 1.7.6: C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O)O)O)O)O
  ACDLabs 12.01: OC1C(O)C(OC(O)C1O)CO
• Formula: C6 H12 O6
• Name: beta-D-glucopyranose;
  beta-D-glucose;
  D-glucose;
  glucose
• ChEMBL: CHEMBL1614854
• DrugBank: DB02379
• ZINC: ZINC000003833800
• PDB chain: 5dvi Chain B Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5dvi High Resolution Structures of Periplasmic Glucose-binding Protein of Pseudomonas putida CSV86 Reveal Structural Basis of Its Substrate Specificity
• Resolution: 1.25 Å
• Binding residue (original residue number in PDB): W35 E41 G67 G68 K92 W270 N301 D303 K339 H379
• Binding residue (residue number reindexed from 1): W10 E16 G42 G43 K67 W245 N276 D278 K314 H354
• Annotation score: 4
• Binding affinity: MOAD: Kd=0.39uM

External links

• PDB: RCSB:5dvi, PDBe:5dvi, PDBj:5dvi
• PDBsum: 5dvi
• PubMed: 26861882
• UniProt: H7BRJ8