Structure of PDB 5jy6 Chain D Binding Site BS02

Receptor Information

>5jy6 Chain D (length=333) Species: 1311 (Streptococcus agalactiae)

VKVGINGFGRIGRLAFRRIQNVEGVEVTRINDLTDPNMLAHLLKYDTTQG
RFDGTVEVKEGGFEVNGQFVKVSAEREPANIDWATDGVEIVLEATGFFAS
KEKAEQHIHENGAKKVVITAPGGNDVKTVVFNTNHDILDGTETVISGASC
TTNCLAPMAKALQDNFGVKQGLMTTIHAYTGDQMILDGPHRGGDLRRARA
GAANIVPNSTGAAKAIGLVIPELNGKLDGAAQRVPVPTGSVTELVATLEK
DVTVEEVNAAMKAAANDSYGYTEDPIVSSDIVGISYGSLFDATQTKVQTV
DGNQLVKVVSWYDNEMSYTSQLVRTLEYFAKIA

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 5jy6 Chain D Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5jy6 Crystal Structures of Group B Streptococcus Glyceraldehyde-3-Phosphate Dehydrogenase: Apo-Form, Binary and Ternary Complexes.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): I21 V24 V27
• Binding residue (residue number reindexed from 1): I19 V22 V25
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): C152 H179
• Catalytic site (residue number reindexed from 1): C150 H177
• Enzyme Commision number: 1.2.1.-

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0004365 glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
• GO:0016491 oxidoreductase activity
• GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
• GO:0042802 identical protein binding
• GO:0046872 metal ion binding
• GO:0050661 NADP binding
• GO:0051287 NAD binding

Biological Process

• GO:0006006 glucose metabolic process
• GO:0006096 glycolytic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:5jy6, PDBe:5jy6, PDBj:5jy6
• PDBsum: 5jy6
• PubMed: 27875551
• UniProt: Q9ALW2