Structure of PDB 6gvd Chain A Binding Site BS01

Receptor Information

>6gvd Chain A (length=531) Species: 243274 (Thermotoga maritima MSB8)

GSHMASMEIFGKTFREGRFVLKEKNFTVEFAVEKIHLGWKISGRVKGSPG
RLEVLRTKAPEKVLVNNWQSWGPCRVVDAFSFKPPEIDPNWRYTASVVPD
VLERNLQSDYFVAEEGKVYGFLSSKIAHPFFAVEDGELVAYLEYFDVEFD
DFVPLEPLVVLEDPNTPLLLEKYAELVGMENNARVPKHTPTGWCSWYHYF
LDLTWEETLKNLKLAKNFPFEVFQIDDAYEKDIGDWLVTRGDFPSVEEMA
KVIAENGFIPGIWTAPFSVSETSDVFNEHPDWVVKENGEPKMAYRNWNKK
IYALDLSKDEVLNWLFDLFSSLRKMGYRYFKIDFLFAGAVPGERKKNITP
IQAFRKGIETIRKAVGEDSFILGCGSPLLPAVGCVDGMRIGPDTAPFWGE
HIEDNGAPAARWALRNAITRYFMHDRFWLNDPDCLILREEKTDLTQKEKE
LYSYTCGVLDNMIIESDDLSLVRDHGKKVLKETLELLGGRPRVQNIMSED
LRYEIVSSGTLSGNVKIVVDLNSREYHLEKE

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: 6gvd Chain A Residue 603

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6gvd Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level.
• Resolution: 1.22 Å
• Binding residue (original residue number in PDB): D419 D454
• Binding residue (residue number reindexed from 1): D425 D460
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.2.1.22: alpha-galactosidase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0004557 alpha-galactosidase activity
• GO:0016798 hydrolase activity, acting on glycosyl bonds
• GO:0030246 carbohydrate binding
• GO:0042803 protein homodimerization activity

Biological Process

• GO:0005975 carbohydrate metabolic process
• GO:0016139 glycoside catabolic process

External links

• PDB: RCSB:6gvd, PDBe:6gvd, PDBj:6gvd
• PDBsum: 6gvd
• PubMed: 30104598
• UniProt: G4FEF4|AGAL_THEMA Alpha-galactosidase (Gene Name=galA)