Structure of PDB 4do5 Chain A

Receptor sequence

>4do5A (length=387) Species: 9606 (Homo sapiens)

LDNGLLQTPPMGWLAWERFRCNINCDEDPKNCISEQLFMEMADRMAQDGW
RDMGYTYLNIDDCWIGGRDASGRLMPDPKRFPHGIPFLADYVHSLGLKLG
IYADMGNFTCMGYPGTTLDKVVQDAQTFAEWKVDMLKLDGCFSTPEERAQ
GYPKMAAALNATGRPIAFSCSWPAYEGGLPPRVQYSLLADICNLWRNYDD
IQDSWWSVLSILNWFVEHQDILQPVAGPGHWNDPDMLLIGNFGLSLEQSR
AQMALWTVLAAPLLMSTDLRTISAQNMDILQNPLMIKINQDPLGIQGRRI
HKEKSLIEVYMRPLSNKASALVFFSCRTDMPYRYHSSLGQLNFTGSVIYE
AQDVYSGDIISGLRDETNFTVIINPSGVVMWYLYPIK

3D structure

• PDB: 4do5 Pharmacological chaperones for human alpha-N-acetylgalactosaminidase
• Chain: A
• Resolution: 1.51 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D156 D217
• Catalytic site (residue number reindexed from 1): D139 D200
• Enzyme Commision number: 3.2.1.49: alpha-N-acetylgalactosaminidase.

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	DGJ	A	W33 D78 D79 C127 K154 D156 R213 D217	W16 D61 D62 C110 K137 D139 R196 D200	PDBbind-CN: -logKd/Ki=5.83,Ki=1.48uM

Gene Ontology

Molecular Function

• GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
• GO:0004557 alpha-galactosidase activity
• GO:0008456 alpha-N-acetylgalactosaminidase activity
• GO:0016798 hydrolase activity, acting on glycosyl bonds
• GO:0042803 protein homodimerization activity

Biological Process

• GO:0005975 carbohydrate metabolic process
• GO:0006629 lipid metabolic process
• GO:0009311 oligosaccharide metabolic process
• GO:0016052 carbohydrate catabolic process
• GO:0016139 glycoside catabolic process
• GO:0019377 glycolipid catabolic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0005764 lysosome
• GO:0070062 extracellular exosome

External links

• PDB: RCSB:4do5, PDBe:4do5, PDBj:4do5
• PDBsum: 4do5
• PubMed: 23045655
• UniProt: P17050|NAGAB_HUMAN Alpha-N-acetylgalactosaminidase (Gene Name=NAGA)