Structure of PDB 8xhk Chain D Binding Site BS01

Receptor Information

>8xhk Chain D (length=395) Species: 1093098 (Streptomyces albogriseolus 1-36)

VKKLRHLSDGYWDSAARLGVHGAVLQAVPGGRLSAPDGRVAVNMSSYSYL
GLDESPRIIDAAIAALRSNMVLNSSLGRVRMTLPLLEEAECALGDLFGAD
VATLNSCSAAAWATLPVLASGLLTDGVAPVMVFDKRAHFCMASLKSLCAD
ETRVETIRHNDVDALADICRKNKRVAYVCDSVYSTGGTLAPLEELFALQK
EFGLFLYFDEAHSTSVIGDMGRGYVLDRMGAINDSTMLITSLNKGFGASG
GAIVFGPRDDDRKRKIIQRSSGPLMWSQRLNTPALGAIIESAKLHRSEAL
PELQAKLHSNIALFDGLVRAAGQGNSVPIRYLELGSEVDTLEASAYLFDN
GFYVEPDFFPIVSRGAAGLRARIRSSMSTADIEQFAHVWHKLGVD

Ligand information

• Ligand ID: PLR
• InChI: InChI=1S/C8H12NO5P/c1-5-7(4-14-15(11,12)13)3-9-6(2)8(5)10/h3,10H,4H2,1-2H3,(H2,11,12,13)
• InChIKey: RBCOYOYDYNXAFA-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: Cc1ncc(CO[P](O)(O)=O)c(C)c1O
  ACDLabs 10.04: O=P(O)(O)OCc1cnc(c(O)c1C)C
  OpenEye OEToolkits 1.5.0: Cc1c(cnc(c1O)C)COP(=O)(O)O
• Formula: C8 H12 N O5 P
• Name: (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE;
  4'-DEOXYPYRIDOXINE PHOSPHATE
• ChEMBL: CHEMBL1235333
• ZINC: ZINC000001656021
• PDB chain: 8xhk Chain D Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8xhk Structural and mechanistic investigations on CC bond forming alpha-oxoamine synthase allowing L-glutamate as substrate.
• Resolution: 2.79 Å
• Binding residue (original residue number in PDB): S116 C117 S118 H148 D219 A221 H222 S251 K254
• Binding residue (residue number reindexed from 1): S106 C107 S108 H138 D209 A211 H212 S241 K244
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.3.1.47: 8-amino-7-oxononanoate synthase.

Gene Ontology

Molecular Function

• GO:0008483 transaminase activity
• GO:0030170 pyridoxal phosphate binding

Biological Process

• GO:0009058 biosynthetic process

External links

• PDB: RCSB:8xhk, PDBe:8xhk, PDBj:8xhk
• PDBsum: 8xhk
• PubMed: 38642679
• UniProt: A0A6B9KSL0