Structure of PDB 4zm3 Chain A Binding Site BS02

Receptor Information

>4zm3 Chain A (length=389) Species: 68249 (Streptomyces pactum)

LPLVVRSAGGCLLRDVEDGEIIDLNMGYGPHLFGYADREVLDAVADQFAK
GHMTGLPHELDARAGALIAELVPGVEQVRFANSGTEAVASALRLARATTG
RTLVVTFEGHYHGWSETVLRAGKTATRPTDVVPGALGMIPEALAHTVQLG
WNDPDALRELFARDGDRIAAVIVEPVLANAGVIPPAPGFLQLLRELTGRS
GAMLVFDEVITGFRVARGGAQERYGVEPDLTVLSKVMGGGFPVAAFGGRR
HAMRMAGVYAGNHAALRAVVAMLGKIRSLPDLYERLEDTGQYMEDTVREV
FATEKRPVHINRVGTLMSVALLKGSEPRDLRQLAALVDFPRHRRLQTLAQ
KEGVYFHPNALEPWFLSTAHTRDVIDKVAGALQRSLVGL

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: 4zm3 Chain B Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4zm3 Mechanism-Based Trapping of the Quinonoid Intermediate by Using the K276R Mutant of PLP-Dependent 3-Aminobenzoate Synthase PctV in the Biosynthesis of Pactamycin.
• Resolution: 2.27 Å
• Binding residue (original residue number in PDB): G306 V307
• Binding residue (residue number reindexed from 1): G257 V258
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): Y147 E215 D248 I251 K276 P417
• Catalytic site (residue number reindexed from 1): Y111 E174 D207 I210 K235 P363

Gene Ontology

Molecular Function

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

Biological Process

• GO:0009058 biosynthetic process

External links

• PDB: RCSB:4zm3, PDBe:4zm3, PDBj:4zm3
• PDBsum: 4zm3
• PubMed: 26426567
• UniProt: A8R0K5