Structure of PDB 8apz Chain A Binding Site BS06

Receptor Information

>8apz Chain A (length=412) Species: 382 (Sinorhizobium meliloti)

GENRRVNADRLWDSLMEMAKIGPGVAGGNNRQTLTDADGEGRRLFQSWCE
EAGLSMGVDKMGTMFLTRPGTDPDALPVHIGSHLDTQPTGGKFDGVLGVL
SGLEAVRTMNDLGIKTKHPIVVTNWTNEEGARFAPAMLASGVFAGVHTLE
YAYARKDPEGKSFGDELKRIGWLGDEEVGARKMHAYFEYHIEQGPILEAE
NKQIGVVTHCQGLWWLEFTLTGREAHTGSTPMDMRVNAGLAMARILEMVQ
TVAMENQPGAVGGVGQMFFSPNSRNVLPGKVVFTVDIRSPDQAKLDGMRA
RIEAEAPKICERLGVGCSIEAVGHFDPVTFDPKLVETVRGAAEKLGYSHM
NLVSGAGHDACWAAKVAPTTMIMCPCVGGLSHNEAEDISREWAAAGADVL
FHAVLETAEIVE

Ligand information

• Ligand ID: ORD
• InChI: InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m1/s1
• InChIKey: AHLPHDHHMVZTML-SCSAIBSYSA-N
• SMILES:
  OpenEye OEToolkits 1.6.1: C(C[C@H](C(=O)O)N)CN
  CACTVS 3.352: NCCC[CH](N)C(O)=O
  ACDLabs 10.04: O=C(O)C(N)CCCN
  CACTVS 3.352: NCCC[C@@H](N)C(O)=O
  OpenEye OEToolkits 1.6.1: C(CC(C(=O)O)N)CN
• Formula: C5 H12 N2 O2
• Name: D-ORNITHINE
• ChEMBL: CHEMBL103686
• ZINC: ZINC000001532678
• PDB chain: 8apz Chain B Residue 505

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8apz Selecting Better Biocatalysts by Complementing Recoded Bacteria.
• Resolution: 1.75 Å
• Binding residue (original residue number in PDB): H230 N279
• Binding residue (residue number reindexed from 1): H226 N275
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.5.1.87: N-carbamoyl-L-amino-acid hydrolase.

Gene Ontology

Molecular Function

• GO:0016787 hydrolase activity
• GO:0016813 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines
• GO:0046872 metal ion binding
• GO:0050538 N-carbamoyl-L-amino-acid hydrolase activity

Biological Process

• GO:0008652 amino acid biosynthetic process

External links

• PDB: RCSB:8apz, PDBe:8apz, PDBj:8apz
• PDBsum: 8apz
• PubMed: 36342942
• UniProt: Q6DTN4|HYUC_RHIML N-carbamoyl-L-amino-acid hydrolase (Gene Name=hyuC)