Structure of PDB 5m6d Chain A Binding Site BS01

Receptor Information

>5m6d Chain A (length=346) Species: 1313 (Streptococcus pneumoniae)

HHHQLENLYFQGVVKVGINGFGRIGRLAFRRIQNVEGVEVTRINDLTDPV
MLAHLLKYDTTQGRFDGTVEVKEGGFEVNGKFIKVSAERDPEQIDWATDG
VEIVLEATGFFAKKEAAEKHLKGGAKKVVITAPGGNDVKTVVFNTNHDVL
DGTETVISGASCTTNCLAPMAKALQDNFGVVEGLMTTIHAYTGDQMILDG
PHRGGDLRRARAGAANIVPNSTGAAKAIGLVIPELNGKLDGSAQRVPTPT
GSVTELVAVLEKNVTVDEVNAAMKAASNESYGYTEDPIVSSDIVGMSYGS
LFDATQTKVLDVDGKQLVKVVSWYDNEMSYTAQLVRTLEYFAKIAK

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: 5m6d Chain A Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5m6d Deciphering Key Residues Involved in the Virulence-promoting Interactions between Streptococcus pneumoniae and Human Plasminogen.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): I41 Q42 V44 V47
• Binding residue (residue number reindexed from 1): I32 Q33 V35 V38
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): C171 H198
• Catalytic site (residue number reindexed from 1): C162 H189
• 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:0046872 metal ion binding
• GO:0050661 NADP binding
• GO:0051287 NAD binding

Biological Process

• GO:0006006 glucose metabolic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:5m6d, PDBe:5m6d, PDBj:5m6d
• PDBsum: 5m6d
• PubMed: 28011643
• UniProt: I6L8L9