Structure of PDB 5dmy Chain A Binding Site BS01

Receptor Information
>5dmy Chain A (length=855) Species: 1681 (Bifidobacterium bifidum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSAVDSKQNRTSDFDANWKFMLSDSVQAQDPAFDDSAWQQVDLPHDYSIT
QKYSQSNEAESAYLPGGTGWYRKSFTIDRDLAGKRIAINFDGVYMNATVW
FNGVKLGTHPYGYSPFSFDLTGNAKFGGENTIVVKVENRLPSSRWYSGSG
IYRDVTLTVTDGVHVGNNGVAIKTPSLATQNGGNVTMNLTTKVANDTEAA
ANITLKQTVFPKGGKTDAAIGTVTTASKSIAAGASADVTSTITAASPKLW
SIKNPNLYTVRTEVLNGDTVLDTYDTEYGFRWTGFDATSGFSLNGEKVKL
KGVSMHHDQGSLGAVANRRAIERQVEILQKMGVNSIRTTHNPAAKALIDV
CNEKGVLVVEEVFDMWNRSKNGNTEDYGKWFGQTIAGDNAVLGGDKDETW
AKFDLTSTINRDRNAPSVIMWSLGNEMMEGISGSVSDFPATSAKLVAWTK
AADSTRPMTYGDNKIKANWNESNTMGDNLTANGGVVGTNYSDGANYDKIR
TTHPSWAIYGSETASAINSRGIYNRTTGSDKQLTSYDNSAVGWGAVASSA
WYDVVQRDFVAGTYVWTGFDYLGEPTPWNGTGSGAVGSWPSPKNSYFGIV
DTAGFPKDTYYFYQSQWNDDVHTLHILPAWNENVVAKGSGNKVPVVVYTD
AAKVKLYFTPKGSTEKRLIGEKSFTKKTTAAGYTYQVYEGTDKDSTAHKN
MYLTWNVPWAEGTISAEAYDENNRLIPEGSTEGNASVTTTGKAAKLKADA
DRKTITADGKDLSYIEVDVTDANGHIVPDAANRVTFDVKGAGKLVGVDNG
SSPDHDSYQADNRKAFSGKVLAIVQSTKEAGEITVTAKADGLQSSTVKIA
TTAVP
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain5dmy Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5dmy Rational protein engineering toward the development of a beta-galactosidase with improved functional properties
Resolution1.95 Å
Binding residue
(original residue number in PDB)		N643 V646 D675
Binding residue
(residue number reindexed from 1)		N618 V621 D650
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) R165 H327 H361 M386 N388 E447 Y517 E533 N619 F622
Catalytic site (residue number reindexed from 1) R144 H306 H340 M365 N367 E426 Y496 E512 N594 F597
Enzyme Commision number 3.2.1.23: beta-galactosidase.
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
Biological Process
GO:0005975 carbohydrate metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5dmy, PDBe:5dmy, PDBj:5dmy
PDBsum5dmy
PubMed
UniProtD4QAP3

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