Structure of PDB 7dmk Chain B Binding Site BS01

Receptor Information
>7dmk Chain B (length=732) Species: 626929 (Bacteroides clarus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RTIDLNSLQSTLEKAGPGDTIYIKSGTYTNIQLQLEGYGKVEEPIVVMAQ
QPGSVFIEGVSNLRLCGEYVEINGLHFRNGYTPKGAVIEFRNGEKVANNC
RITDCVIDYFNPIDRGVSGSWILLYGRNNRLDHNSILGKLYAGVTLAVIL
NGEGDRNNNHRIDHNYFGERPILGSNGGETIRVGTSHHAFFSSNTVIEDN
MFHHCNGEVEVVSIKSSDNIIRNNVFLECRGILALRHGNRNLVEGNAFIG
NGLPCTGGVRIVNEGHTIKGNLFYGLKGDRFFAALGLMNAVPNSLPNRYH
HVKDVTLEDNRFINCDNILFCVGKDNERTLPPSNISFIRNQFISKSDKAL
YQSFDDISGFTFIDNVVNYPYTVTQRGFQNNTTLSDSIDLKPYMEKKNGA
SWYTLSELVLTGNEISVKAGQNTLLEALNQAQSGDILNLSEEGVYWLDNT
LLIDKYIRIQADSHLSKRPVLCFNGMSGKAFVTIVNGGNLEIQGLAFNGE
GEAGKALSEGGITVKSGTITPYLLTVDNCEFYNFNESGLAAIRGEKSTFS
PMVIIRNSFFHDMSGEAINFAGEKDDKGKYNVEELHVDNCIFYRLLGSAL
NIYRGGNDESTSGPLLTVDHCTIENVDNKEQGSAMRLIGVQSATVTNCSF
ANSGKGGASIRFNEMSWDKLSVSYINLYNSGRIASFWGKLGSKNITNYRP
EYVDANTGNFYQISTSPLSNKASDKKDLGITQ
Ligand information
Ligand IDCA
InChIInChI=1S/Ca/q+2
InChIKeyBHPQYMZQTOCNFJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Ca++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Ca+2]
FormulaCa
NameCALCIUM ION
ChEMBL
DrugBankDB14577
ZINC
PDB chain7dmk Chain B Residue 801 [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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PDB7dmk Structural basis for the exolytic activity of polysaccharide lyase family 6 alginate lyase BcAlyPL6 from human gut microbe Bacteroides clarus.
Resolution2.213 Å
Binding residue
(original residue number in PDB)		N188 E191 E220 E222
Binding residue
(residue number reindexed from 1)		N176 E179 E208 E210
Annotation score1
Enzymatic activity
Enzyme Commision number 3.2.1.22: alpha-galactosidase.
3.2.1.n1: blood group B branched chain alpha-1,3-galactosidase.
Gene Ontology
Molecular Function
GO:0004557 alpha-galactosidase activity
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:7dmk, PDBe:7dmk, PDBj:7dmk
PDBsum7dmk
PubMed33610038
UniProtA0A1Y4JW59

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