Structure of PDB 5yu3 Chain D Binding Site BS02

Receptor Information

>5yu3 Chain D (length=344) Species: 38300 (Streptomyces pristinaespiralis)

METWVLGRRDVAEVVAAVGRDELMRRIIDRLTGGLAEIGRGERHLSPLRG
GLERSEPVPGIWEWMPHREPGDHITLKTVGYSPANPARFGLPTILGTVAR
YDDTTGALTALMDGVLLTALRTGAASAVASRLLARPDSHTLGLIGTGAQA
VTQLHALSLVLPLQRALVWDTDPAHRESFARRAAFTGVSVEIAEPARIAA
EADVISTATSVAVGQGPVLPDTGVREHLHINAVGADLVGKTELPLGLLER
AFVTADHPEQALREGECQQLSADRLGPQLAHLCADPAAAAGRQDTLSVFD
STGFAFEDALAMEVFLEAAAERDLGIRVGIEHHPGDALDPYALQ

Ligand information

• Ligand ID: PRO
• InChI: InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1
• InChIKey: ONIBWKKTOPOVIA-BYPYZUCNSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C1C[C@H](NC1)C(=O)O
  CACTVS 3.341: OC(=O)[C@@H]1CCCN1
  CACTVS 3.341: OC(=O)[CH]1CCCN1
  OpenEye OEToolkits 1.5.0: C1CC(NC1)C(=O)O
  ACDLabs 10.04: O=C(O)C1NCCC1
• Formula: C5 H9 N O2
• Name: PROLINE
• ChEMBL: CHEMBL54922
• DrugBank: DB00172
• ZINC: ZINC000000895360
• PDB chain: 5yu3 Chain D Residue 403

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5yu3 Structural Basis for Recognition of L-lysine, L-ornithine, and L-2,4-diamino Butyric Acid by Lysine Cyclodeaminase.
• Resolution: 1.79 Å
• Binding residue (original residue number in PDB): M65 K77 R121
• Binding residue (residue number reindexed from 1): M65 K77 R121
• Annotation score: 5

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:5yu3, PDBe:5yu3, PDBj:5yu3
• PDBsum: 5yu3
• PubMed: 29629557
• UniProt: D9UBW0