Structure of PDB 6k38 Chain A Binding Site BS01

Receptor Information

>6k38 Chain A (length=327) Species: 1148 (Synechocystis sp. PCC 6803)

SLAPLRVGILGFGGLGQAAARLLAPKQEMKLVAVADRHGYLYDADGIDVD
NAVQAYTQQGSVGKAKKGQMSEQSIEDLIGEGEVDGYFLALPNLPNTFMA
DVTRQFIASGWQGVLVDALKRTSAVEQLITLREDLAQAGITYMTGCGATP
GLLTAAAAIASQSFQEIHQVKITFGVGIANWEAYRATIREDIAHMPGYNV
DKAQAMTDAEVAALLDQTNGILALEDMEAADDIMLELAGICHRDQVTVGG
VVDTRNPKKPLSTHVKITGRTFEGKISSHTFTLGDETSMAANVCGPAFGY
LKAGYGLHRQGLKGLFTAADVMPKFVR

Ligand information

• Ligand ID: CWF
• InChI: InChI=1S/C9H19NO2/c1-8(10)6-4-2-3-5-7-9(11)12/h8H,2-7,10H2,1H3,(H,11,12)/t8-/m0/s1
• InChIKey: VXBHEKXWXPQBQM-QMMMGPOBSA-N
• SMILES:
  CACTVS 3.385: C[C@H](N)CCCCCCC(O)=O
  OpenEye OEToolkits 2.0.7: C[C@@H](CCCCCCC(=O)O)N
  CACTVS 3.385: C[CH](N)CCCCCCC(O)=O
  OpenEye OEToolkits 2.0.7: CC(CCCCCCC(=O)O)N
• Formula: C9 H19 N O2
• Name: (8S)-8-azanylnonanoic acid
• PDB chain: 6k38 Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6k38 A suicide enzyme catalyzes multiple reactions for biotin biosynthesis in cyanobacteria.
• Resolution: 1.78 Å
• Binding residue (original residue number in PDB): K124 F178 V180 D195 K263 T267 M293 N296
• Binding residue (residue number reindexed from 1): K120 F174 V176 D191 K259 T263 M289 N292
• Annotation score: 2

Enzymatic activity

• Enzyme Commision number: 2.6.1.121: 8-amino-7-oxononanoate carboxylating dehydrogenase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0008483 transaminase activity
• GO:0016491 oxidoreductase activity
• GO:0050661 NADP binding
• GO:0051287 NAD binding

Biological Process

• GO:0006520 amino acid metabolic process
• GO:0009102 biotin biosynthetic process

External links

• PDB: RCSB:6k38, PDBe:6k38, PDBj:6k38
• PDBsum: 6k38
• PubMed: 32042199
• UniProt: Q55650|BIOU_SYNY3 (S)-8-amino-7-oxononanoate synthase BioU (Gene Name=bioU)