Structure of PDB 6gvd Chain A

Receptor sequence

>6gvdA (length=531) Species: 243274 (Thermotoga maritima MSB8)

GSHMASMEIFGKTFREGRFVLKEKNFTVEFAVEKIHLGWKISGRVKGSPG
RLEVLRTKAPEKVLVNNWQSWGPCRVVDAFSFKPPEIDPNWRYTASVVPD
VLERNLQSDYFVAEEGKVYGFLSSKIAHPFFAVEDGELVAYLEYFDVEFD
DFVPLEPLVVLEDPNTPLLLEKYAELVGMENNARVPKHTPTGWCSWYHYF
LDLTWEETLKNLKLAKNFPFEVFQIDDAYEKDIGDWLVTRGDFPSVEEMA
KVIAENGFIPGIWTAPFSVSETSDVFNEHPDWVVKENGEPKMAYRNWNKK
IYALDLSKDEVLNWLFDLFSSLRKMGYRYFKIDFLFAGAVPGERKKNITP
IQAFRKGIETIRKAVGEDSFILGCGSPLLPAVGCVDGMRIGPDTAPFWGE
HIEDNGAPAARWALRNAITRYFMHDRFWLNDPDCLILREEKTDLTQKEKE
LYSYTCGVLDNMIIESDDLSLVRDHGKKVLKETLELLGGRPRVQNIMSED
LRYEIVSSGTLSGNVKIVVDLNSREYHLEKE

3D structure

• PDB: 6gvd Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level.
• Chain: A
• Resolution: 1.22 Å

Enzymatic activity

• Enzyme Commision number: 3.2.1.22: alpha-galactosidase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	MG	A	D419 D454	D425 D460
BS02	MG	A	R383 I384 G385 D425 P426 D427	R389 I390 G391 D431 P432 D433
BS03	FDK	A	W65 W190 Y191 D220 D221 W257 K325 D327 F328 C368 R383 D387	W71 W196 Y197 D226 D227 W263 K331 D333 F334 C374 R389 D393

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)