Structure of PDB 5z83 Chain B Binding Site BS01

Receptor Information

>5z83 Chain B (length=408) Species: 1877 (Micromonospora echinospora)

KLLAQEPTCPRDADGRPRVFVEGSGAYLTDPDGRRWIDFDNARGSVVLGH
GDEEVAEAIARAARGRSGVGTAWSPVLDSLLGQLQEVCGGDVVGLYRTGT
AALRSVTCAVRDARDRSIVLSSGYHGYDPMWHCDEPFTPNQHGIVEFLFD
LDVLAEWLSRPEQVAAVVISPDHMHLGERWYTEFTRLTKEADVPVIADEV
KVGLRYRAGLSTPLLDPAVWIVAKCLANGSPVAAVGGDAHLLAALEDVSF
TSYFEPTAMAAATTTLRRMATGEPQQAIRAAGDRFIAHTRAAFANAGVPI
DLAGNGNLFQFVCADDEVADAFHAAAAAEGLLFFEGDNQTPSAAFTDEVV
EDACGRIDRVSAALTGRFTDRELTEESWYASAWGAMDGLADRPRTREETT
AIVERLWE

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: 5z83 Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5z83 Complete reconstitution of the diverse pathways of gentamicin B biosynthesis.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): F258 T259
• Binding residue (residue number reindexed from 1): F250 T251
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): Y132 D206 K232
• Catalytic site (residue number reindexed from 1): Y124 D198 K224

Gene Ontology

Molecular Function

• GO:0008483 transaminase activity
• GO:0030170 pyridoxal phosphate binding
• GO:0046872 metal ion binding

External links

• PDB: RCSB:5z83, PDBe:5z83, PDBj:5z83
• PDBsum: 5z83
• PubMed: 30643280
• UniProt: Q70KD9