Structure of PDB 5v2l Chain A Binding Site BS02

Receptor Information

>5v2l Chain A (length=321) Species: 226185 (Enterococcus faecalis V583)

AMLSGKARAHTNIALIKYWGKANEEYILPMNSSLSLTLDAFYTETTVTFD
AHYSEDVFILNGILQNEKQTKKVKEFLNLVRQQADCTWFAKVESQNFVPT
AAGLASSASGLAALAGACNVALGLNLSAKDLSRLARRGSGSACRSIFGGF
AQWNKGHSDETSFAENIPANNWENELAMLFILINSSRDGMKRTVETSSFY
QGWLDNVEKDLSQVHEAIKTKDFPRLGEIIEANGLRMHGTTLGAVPPFTY
WSPGSLQAMALVRQARAKGIPCYFTMDAGPNVKVLVEKKNLEALKTFLSE
HFSKEQLVPAFAGPGIELFET

Ligand information

• Ligand ID: PO4
• InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
• InChIKey: NBIIXXVUZAFLBC-UHFFFAOYSA-K
• SMILES:
  CACTVS 3.341: [O-][P]([O-])([O-])=O
  ACDLabs 10.04: [O-]P([O-])([O-])=O
  OpenEye OEToolkits 1.5.0: [O-]P(=O)([O-])[O-]
• Formula: O4 P
• Name: PHOSPHATE ION
• DrugBank: DB14523
• PDB chain: 5v2l Chain A Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5v2l Mevalonate 5-diphosphate mediates ATP binding to the mevalonate diphosphate decarboxylase from the bacterial pathogen Enterococcus faecalis.
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): Y17 K20 G139 R192
• Binding residue (residue number reindexed from 1): Y18 K21 G140 R187
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 4.1.1.33: diphosphomevalonate decarboxylase.

Gene Ontology

Molecular Function

• GO:0004163 diphosphomevalonate decarboxylase activity
• GO:0005524 ATP binding
• GO:0016301 kinase activity
• GO:0016829 lyase activity
• GO:0016831 carboxy-lyase activity

Biological Process

• GO:0006629 lipid metabolic process
• GO:0008299 isoprenoid biosynthetic process
• GO:0016310 phosphorylation
• GO:0019287 isopentenyl diphosphate biosynthetic process, mevalonate pathway

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:5v2l, PDBe:5v2l, PDBj:5v2l
• PDBsum: 5v2l
• PubMed: 29025876
• UniProt: Q837E0