Structure of PDB 8yrt Chain A Binding Site BS01

Receptor Information

>8yrt Chain A (length=282) Species: 760192 (Haliscomenobacter hydrossis DSM 1100)

HMIKYYNINGQQVPVENATLHVSDLSILRGYGIFDYFLAREGHPLFLDDY
LNRFYRSAAELYLEIPFDKAELRRQIYALLQANEVREAGIRLVLTGGYSP
DGYTPVNPNLLIMMYDLPASAWEFSAQGIKIITHPFQRELPEVKTINYST
GIRMLKTIKERGATDLIYVDQGEWIRESARSNFFLVMPDNTIVTADEKIL
WGITRRQVIDAAREAGYAVEERRIHITELDQAREAFFTSTIKGVMAIGQI
DDRVFGDGTIGKVTQELQDLFVGKVKAYLETC

Ligand information

• Ligand ID: PLP
• InChI: InChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)
• InChIKey: NGVDGCNFYWLIFO-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O
  OpenEye OEToolkits 1.5.0: Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
  ACDLabs 10.04: O=P(O)(O)OCc1cnc(c(O)c1C=O)C
• Formula: C8 H10 N O6 P
• Name: PYRIDOXAL-5'-PHOSPHATE;
  VITAMIN B6 Phosphate
• ChEMBL: CHEMBL82202
• DrugBank: DB00114
• ZINC: ZINC000001532514
• PDB chain: 8yrt Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8yrt Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis in the holo form obtained at pH 7.0
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): R52 R137 K143 Y147 E176 A178 R179 S180 N181 L199 G201 I202 T203 S238 T239
• Binding residue (residue number reindexed from 1): R53 R138 K144 Y148 E177 A179 R180 S181 N182 L200 G202 I203 T204 S239 T240
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0008483 transaminase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0019752 carboxylic acid metabolic process
• GO:0046394 carboxylic acid biosynthetic process

External links

• PDB: RCSB:8yrt, PDBe:8yrt, PDBj:8yrt
• PDBsum: 8yrt
• UniProt: F4KWH0