Structure of PDB 5d56 Chain D Binding Site BS02

Receptor Information

>5d56 Chain D (length=108) Species: 83333 (Escherichia coli K-12)

AGYSWKGLRAAWINEAAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVM
LVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWA
ILLWSHFG

Ligand information

• Ligand ID: ZN
• InChI: InChI=1S/Zn/q+2
• InChIKey: PTFCDOFLOPIGGS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Zn++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Zn+2]
• Formula: Zn
• Name: ZINC ION
• ChEMBL: CHEMBL1236970
• DrugBank: DB14532
• PDB chain: 5d56 Chain D Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5d56 In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): E28 E76
• Binding residue (residue number reindexed from 1): E15 E63
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.7.1.107: diacylglycerol kinase (ATP).

Gene Ontology

Molecular Function

• GO:0004143 ATP-dependent diacylglycerol kinase activity
• GO:0005524 ATP binding
• GO:0016301 kinase activity
• GO:0042802 identical protein binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006654 phosphatidic acid biosynthetic process
• GO:0008610 lipid biosynthetic process
• GO:0008654 phospholipid biosynthetic process
• GO:0009411 response to UV
• GO:0016310 phosphorylation

Cellular Component

• GO:0005886 plasma membrane
• GO:0016020 membrane

External links

• PDB: RCSB:5d56, PDBe:5d56, PDBj:5d56
• PDBsum: 5d56
• PubMed: 26894538
• UniProt: P0ABN1|KDGL_ECOLI Diacylglycerol kinase (Gene Name=dgkA)