Structure of PDB 5yu1 Chain D Binding Site BS02

Receptor Information

>5yu1 Chain D (length=344) Species: 38300 (Streptomyces pristinaespiralis)

METWVLGRRDVAEVVAAVGRDELMRRIIDRLTGGLAEIGRGERHLSPLRG
GLERSEPVPGIWEWMPHREPGDHITLKTVGYSPANPARFGLPTILGTVAR
YDDTTGALTALMDGVLLTALRTGAASAVASRLLARPDSHTLGLIGTGAQA
VTQLHALSLVLPLQRALVWDTDPAHRESFARRAAFTGVSVEIAEPARIAA
EADVISTATSVAVGQGPVLPDTGVREHLHINAVGADLVGKTELPLGLLER
AFVTADHPEQALREGECQQLSADRLGPQLAHLCADPAAAAGRQDTLSVFD
STGFAFEDALAMEVFLEAAAERDLGIRVGIEHHPGDALDPYALQ

Ligand information

• Ligand ID: YCP
• InChI: InChI=1S/C6H11NO2/c8-6(9)5-3-1-2-4-7-5/h5,7H,1-4H2,(H,8,9)/t5-/m0/s1
• InChIKey: HXEACLLIILLPRG-YFKPBYRVSA-N
• SMILES:
  CACTVS 3.352: OC(=O)[C@@H]1CCCCN1
  OpenEye OEToolkits 1.7.0: C1CCNC(C1)C(=O)O
  OpenEye OEToolkits 1.7.0: C1CCN[C@@H](C1)C(=O)O
  CACTVS 3.352: OC(=O)[CH]1CCCCN1
• Formula: C6 H11 N O2
• Name: (2S)-piperidine-2-carboxylic acid
• ChEMBL: CHEMBL322883
• ZINC: ZINC000000157015
• PDB chain: 5yu1 Chain D Residue 403

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5yu1 Structural Basis for Recognition of L-lysine, L-ornithine, and L-2,4-diamino Butyric Acid by Lysine Cyclodeaminase.
• Resolution: 1.923 Å
• Binding residue (original residue number in PDB): R49 E63 M65 K77 R121 A235 T302
• Binding residue (residue number reindexed from 1): R49 E63 M65 K77 R121 A235 T302
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 4.3.1.12: ornithine cyclodeaminase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0008473 ornithine cyclodeaminase activity
• GO:0016829 lyase activity

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:5yu1, PDBe:5yu1, PDBj:5yu1
• PDBsum: 5yu1
• PubMed: 29629557
• UniProt: D9UBW0