Structure of PDB 5hc8 Chain A Binding Site BS02

Receptor Information

>5hc8 Chain A (length=236) Species: 39330 (Lavandula lanata)

DEVTPNHVAIIIDGHRKWAKSRGVTVQEGHQTGVNNWKHIISRASQLGIK
LLTIWALSPQNFNRSKMEVDFLMRIYEDFLRSDVKELVTSQQDIQFSAIG
DKSRLPEYLQDAISYAEGLSQANKGMHFILAVAYGGREDIVEAARKIAAK
VEHGILRPDDIDEATFEQHLMTNITKFPSPDLLIRAAGEQRLSNFFLWQL
PFTEFYFTPKLFPDFGEADLLDALASYRCRYRGFGE

Ligand information

• Ligand ID: 61G
• InChI: InChI=1S/C5H8/c1-4-5(2)3/h4H,1-2H2,3H3
• InChIKey: RRHGJUQNOFWUDK-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385
  OpenEye OEToolkits 2.0.4: CC(=C)C=C
  ACDLabs 12.01: C\C(=C)[C@H]=C
• Formula: C5 H8
• Name: 2-methylbuta-1,3-diene
• ChEMBL: CHEMBL1566132
• ZINC: ZINC000001699876
• PDB chain: 5hc8 Chain A Residue 403

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5hc8 Structure and Function of a "Head-to-Middle" Prenyltransferase: Lavandulyl Diphosphate Synthase
• Resolution: 1.87 Å
• Binding residue (original residue number in PDB): H78 A119 N124 R127
• Binding residue (residue number reindexed from 1): H15 A56 N61 R64
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D76 H93 M189
• Catalytic site (residue number reindexed from 1): D13 H30 M126
• Enzyme Commision number: 2.5.1.-

Gene Ontology

Molecular Function

• GO:0002094 polyprenyltransferase activity
• GO:0016740 transferase activity
• GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups
• GO:0045547 dehydrodolichyl diphosphate synthase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0009409 response to cold
• GO:0009668 plastid membrane organization
• GO:0016094 polyprenol biosynthetic process

Cellular Component

• GO:0009570 chloroplast stroma

External links

• PDB: RCSB:5hc8, PDBe:5hc8, PDBj:5hc8
• PDBsum: 5hc8
• PubMed: 26922900
• UniProt: A0A140UHQ1