Structure of PDB 5agd Chain B Binding Site BS05

Receptor Information

>5agd Chain B (length=344) Species: 1397 (Niallia circulans)

HHHHHSSASDGDTAMKAFNDTFWDPNAKMFWKDSKREKHQDFWVEAELWE
LVMDAYQHTSDPALKAELKTQIDDVYDGTVAKYGQDWTNNPFNDNIMWWA
MGSARAYQITGNPRYLEAARDHFDFVYDTQWDEEFANGGIWWLNSDHNTK
NACINFPAAQAALYLYDITKDEHYLNAATKIFRWGKTMLTDGNGKVFDRI
EIEHGAVPDATHYNQGTYIGSAVGLYKATGNAVYLDDAVKAAKFTKNHLV
DSNGVLNYEGPNGDLKGGKTILMRNLAHLQKTLDETGQYPEFSAEFDEWL
AFNIEMAWSHQNSDHIVDGNWAGQLLSGTYESWSSAAAVQALNG

Ligand information

• Ligand ID: MAN
• 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-PQMKYFCFSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C(C1C(C(C(C(O1)O)O)O)O)O
  CACTVS 3.341: OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
  CACTVS 3.341: OC[C@H]1O[C@H](O)[C@@H](O)[C@@H](O)[C@@H]1O
  OpenEye OEToolkits 1.5.0: C([C@@H]1[C@H]([C@@H]([C@@H]([C@H](O1)O)O)O)O)O
  ACDLabs 10.04: OC1C(O)C(OC(O)C1O)CO
• Formula: C6 H12 O6
• Name: alpha-D-mannopyranose;
  alpha-D-mannose;
  D-mannose;
  mannose
• ChEMBL: CHEMBL365590
• ZINC: ZINC000003860903
• PDB chain: 5agd Chain B Residue 500A

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5agd Evidence for a Boat Conformation at the Transition State of Gh76 Alpha-1,6-Mannanases- Key Enzymes in Bacterial and Fungal Mannoprotein Metabolism
• Resolution: 1.2 Å
• Binding residue (original residue number in PDB): D71 W73 F122 N125 D294
• Binding residue (residue number reindexed from 1): D41 W43 F92 N95 D264
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 3.2.1.101: mannan endo-1,6-alpha-mannosidase.

Gene Ontology

Biological Process

• GO:0005975 carbohydrate metabolic process

External links

• PDB: RCSB:5agd, PDBe:5agd, PDBj:5agd
• PDBsum: 5agd
• PubMed: 25772148
• UniProt: Q9Z4P9