Structure of PDB 4yge Chain D Binding Site BS02

Receptor Information

>4yge Chain D (length=66) Species: 9606 (Homo sapiens)

MSPQELQLHYFKMHDYDGNNLLDGLELSTAITHMSEDELINIIDGVLRDD
DKNNDGYIDYAEFAKS

Ligand information

• Ligand ID: CA
• InChI: InChI=1S/Ca/q+2
• InChIKey: BHPQYMZQTOCNFJ-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Ca++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Ca+2]
• Formula: Ca
• Name: CALCIUM ION
• DrugBank: DB14577
• PDB chain: 4yge Chain D Residue 502

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4yge Crystallographic snapshots of the EF-hand protein MCFD2 complexed with the intracellular lectin ERGIC-53 involved in glycoprotein transport.
• Resolution: 3.05 Å
• Binding residue (original residue number in PDB): D129 N131 D133 Y135 E140
• Binding residue (residue number reindexed from 1): D51 N53 D55 Y57 E62
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0005509 calcium ion binding
• GO:0005515 protein binding
• GO:0046872 metal ion binding

Biological Process

• GO:0015031 protein transport
• GO:0016192 vesicle-mediated transport

Cellular Component

• GO:0005783 endoplasmic reticulum
• GO:0005789 endoplasmic reticulum membrane
• GO:0005793 endoplasmic reticulum-Golgi intermediate compartment
• GO:0005794 Golgi apparatus
• GO:0012507 ER to Golgi transport vesicle membrane
• GO:0033116 endoplasmic reticulum-Golgi intermediate compartment membrane

External links

• PDB: RCSB:4yge, PDBe:4yge, PDBj:4yge
• PDBsum: 4yge
• PubMed: 32356523
• UniProt: Q8NI22|MCFD2_HUMAN Multiple coagulation factor deficiency protein 2 (Gene Name=MCFD2)