Structure of PDB 4d4d Chain A Binding Site BS02

Receptor Information

>4d4d Chain A (length=333) Species: 1397 (Niallia circulans)

SDGDTAMKAFNDTFWDPNAKMFWKDSKREKHQDFWVEAELWELVMDAYQH
TSDPALKAELKTQIDDVYDGTVAKYGQDWTNNPFNDDIMWWAMGSARAYQ
ITGNPRYLEAARDHFDFVYDTQWDEEFANGGIWWLNSDHNTKNACINFPA
AQAALYLYDITKDEHYLNAATKIFRWGKTMLTDGNGKVFDRIEIEHGAVP
DATHYNQGTYIGSAVGLYKATGNAVYLDDAVKAAKFTKNHLVDSNGVLNY
EGPNGDLKGGKTILMRNLAHLQKTLDETGQYPEFSAEFDEWLAFNIEMAW
SHQNSDHIVDGNWAGQGTYESWSSAAAVQALNG

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: 4d4d Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4d4d Evidence for a Boat Conformation at the Transition State of Gh76 Alpha-1,6-Mannanases- Key Enzymes in Bacterial and Fungal Mannoprotein Metabolism
• Resolution: 1.4 Å
• Binding residue (original residue number in PDB): W172 C183 D228 Y243 L295
• Binding residue (residue number reindexed from 1): W134 C145 D190 Y205 L257
• Annotation score: 4
• Binding affinity: PDBbind-CN: -logKd/Ki=5.96,Kd=1.1uM

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:4d4d, PDBe:4d4d, PDBj:4d4d
• PDBsum: 4d4d
• PubMed: 25772148
• UniProt: Q9Z4P9