Structure of PDB 3k41 Chain B Binding Site BS01

Receptor Information

>3k41 Chain B (length=151) Species: 9913 (Bos taurus)

KTCDLVGEKGKESEKQLALLKRLTPLFQKSFESTVGQSPDMYSYVFRVCR
EAGQHSSGAGLVQIQKSNGKETVVGRFNETQIFQGSNWIMLIYKGGDEYD
NHCGREQRRAVVMISCNRHTLADNFNPVSEERGMVQDCFYLFEMDSSLAC
S

Ligand information

• Ligand ID: M6D
• InChI: InChI=1S/C6H13O9P/c7-3-2(1-14-16(11,12)13)15-6(10)5(9)4(3)8/h2-10H,1H2,(H2,11,12,13)/t2-,3-,4+,5+,6-/m1/s1
• InChIKey: NBSCHQHZLSJFNQ-RWOPYEJCSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C([C@@H]1[C@H]([C@@H]([C@@H]([C@@H](O1)O)O)O)O)OP(=O)(O)O
  CACTVS 3.341: O[CH]1O[CH](CO[P](O)(O)=O)[CH](O)[CH](O)[CH]1O
  CACTVS 3.341: O[C@@H]1O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H](O)[C@@H]1O
  OpenEye OEToolkits 1.5.0: C(C1C(C(C(C(O1)O)O)O)O)OP(=O)(O)O
  ACDLabs 10.04: O=P(O)(O)OCC1OC(O)C(O)C(O)C1O
• Formula: C6 H13 O9 P
• Name: 6-O-phosphono-beta-D-mannopyranose;
  beta-D-mannose-6-phosphate;
  6-O-phosphono-beta-D-mannose;
  6-O-phosphono-D-mannose;
  6-O-phosphono-mannose
• ZINC: ZINC000003869397
• PDB chain: 3k41 Chain B Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3k41 Intermonomer interactions are essential for lysosomal enzyme binding by the cation-dependent mannose 6-phosphate receptor.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): Y45 Q66 Y102 D103 N104 H105 R111 E133 R135 Y143
• Binding residue (residue number reindexed from 1): Y42 Q63 Y99 D100 N101 H102 R108 E130 R132 Y140
• Annotation score: 4
• Binding affinity: MOAD: Kd=150mM

Gene Ontology

Molecular Function

• GO:0019904 protein domain specific binding

Biological Process

• GO:0006622 protein targeting to lysosome

Cellular Component

• GO:0005768 endosome
• GO:0005794 Golgi apparatus

External links

• PDB: RCSB:3k41, PDBe:3k41, PDBj:3k41
• PDBsum: 3k41
• PubMed: 19928875
• UniProt: P11456|MPRD_BOVIN Cation-dependent mannose-6-phosphate receptor (Gene Name=M6PR)