Structure of PDB 5ggk Chain A Binding Site BS01

Receptor Information

>5ggk Chain A (length=153) Species: 9606 (Homo sapiens)

RVLDVEVYSSRSKVYVAVDGTTVLEDEAREQGRGIHVIVLNQATGHVMAK
RVFDTYSPHEDEAMVLFLNMVAPGRVLICTVKDEGSFHLKDTAKALLRSL
GSQAGPALGWRDTWAFVGRKGGPVFGEKHSKSPALSSWGDPVLLKTDVPL
SSA

Ligand information

• Ligand ID: MBE
• InChI: InChI=1S/C12H15NO8/c14-5-8-9(15)10(16)11(17)12(21-8)20-7-3-1-6(2-4-7)13(18)19/h1-4,8-12,14-17H,5H2/t8-,9-,10+,11+,12-/m1/s1
• InChIKey: IFBHRQDFSNCLOZ-LDMBFOFVSA-N
• SMILES:
  OpenEye OEToolkits 2.0.5: c1cc(ccc1[N+](=O)[O-])O[C@H]2[C@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O
  CACTVS 3.385: OC[C@H]1O[C@@H](Oc2ccc(cc2)[N+]([O-])=O)[C@@H](O)[C@@H](O)[C@@H]1O
  OpenEye OEToolkits 2.0.5: c1cc(ccc1[N+](=O)[O-])OC2C(C(C(C(O2)CO)O)O)O
  CACTVS 3.385: OC[CH]1O[CH](Oc2ccc(cc2)[N+]([O-])=O)[CH](O)[CH](O)[CH]1O
• Formula: C12 H15 N O8
• Name: 4-nitrophenyl beta-D-mannopyranoside;
  4-Nitrophenyl-beta-D-mannopyranoside;
  4-nitrophenyl beta-D-mannoside;
  4-nitrophenyl D-mannoside;
  4-nitrophenyl mannoside
• ChEMBL: CHEMBL4462691
• ZINC: ZINC000005842327
• PDB chain: 5ggk Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ggk Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of alpha-dystroglycan
• Resolution: 1.3 Å
• Binding residue (original residue number in PDB): R129 Y152 D179 E180 R207
• Binding residue (residue number reindexed from 1): R33 Y56 D83 E84 R111
• Annotation score: 1
• Binding affinity: MOAD: Kd=0.29mM
  PDBbind-CN: -logKd/Ki=3.54,Kd=0.29mM

Enzymatic activity

• Enzyme Commision number: 2.4.1.-

External links

• PDB: RCSB:5ggk, PDBe:5ggk, PDBj:5ggk
• PDBsum: 5ggk
• PubMed: 27493216
• UniProt: Q8WZA1|PMGT1_HUMAN Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 (Gene Name=POMGNT1)