Structure of PDB 5vxc Chain A Binding Site BS02

Receptor Information

>5vxc Chain A (length=301) Species: 9606 (Homo sapiens)

HKYIPRRAVLYVPGNDEKKIKKIPSLNVDCAVLDCEDGVAANKKNEARLR
IVKTLEDIDLGPTEKCVRVNSVSSGLAEEDLETLLQSRVLPSSLMLPKVE
SPEEIQWFADKFSFHLKGRKLEQPMNLIPFVETAMGLLNFKAVCEETLKV
GPQVGLFLDAVVFGGEDFRASIGATSSKETLDILYARQKIVVIAKAFGLQ
AIDLVYIDFRDGAGLLRQSREGAAMGFTGKQVIHPNQIAVVQEQFSPSPE
KIKWAEELIAAFKEHQQLGKGAFTFQGSMIDMPLLKQAQNTVTLATSIKE
K

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 5vxc Chain A Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5vxc The Human Knockout Gene CLYBL Connects Itaconate to Vitamin B12.
• Resolution: 1.872 Å
• Binding residue (original residue number in PDB): E171 D206
• Binding residue (residue number reindexed from 1): E132 D167
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.3.3.-
  2.3.3.9: malate synthase.
  3.1.2.30: (3S)-malyl-CoA thioesterase.
  4.1.3.25: (S)-citramalyl-CoA lyase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003824 catalytic activity
• GO:0004474 malate synthase activity
• GO:0016740 transferase activity
• GO:0016787 hydrolase activity
• GO:0016829 lyase activity
• GO:0046872 metal ion binding
• GO:0047777 (S)-citramalyl-CoA lyase activity

Biological Process

• GO:0070207 protein homotrimerization
• GO:0106064 regulation of cobalamin metabolic process
• GO:0106121 positive regulation of cobalamin metabolic process

Cellular Component

• GO:0005739 mitochondrion

External links

• PDB: RCSB:5vxc, PDBe:5vxc, PDBj:5vxc
• PDBsum: 5vxc
• PubMed: 29056341
• UniProt: Q8N0X4|CLYBL_HUMAN Citramalyl-CoA lyase, mitochondrial (Gene Name=CLYBL)