Structure of PDB 5ykb Chain B Binding Site BS02

Receptor Information
>5ykb Chain B (length=522) Species: 243230 (Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PEWYKSAVFYELSVRTFQDGNGDGKGDFPGLTSRLDYLKNLGVDCLWLLP
WFPSPLRDDGYDVADYRGIHPDLGTLDDFKVFLREAHARGLWVIGDLVTN
HTSSDHPWFQAARRPNEYHDYYVWSDENWTLDEQAGKYYWHRFFASQPDL
NYDNPKVVEELHGAARFWLDLGLDGFRVDAVPYLIEREGTSCENLPETHE
ILKGFRAMVDREYPGRLLLAEAFQWPEEVVEYFGTEAEPEFHMCFNFPVM
PRLYMSLKREDTSSIREIMGRLPKIPSFGQWCIFLRNHDELTLEMVTDDE
RAFMYAAYAPDARMKINVGIRRRLAPLLDNDRRRIELLNTVLLALPGSPV
LYYGDEIGMGDDLGLPDRNGVRTPMQWNAGTSGGFSTAQPSDCFFPPIQD
PVYGFGRVNVQSQLQDPSSLLKWTARQLELRRAHPAFAHGDLTFIETGNP
AILAFTRQYDGETLLIVSNFAGNAQAGLLDLAPFVGRAPVTLSGASPLPV
VTGNGQYPVVMGKYDYYWLRLN
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 chain5ykb Chain B Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5ykb The N253F mutant structure of trehalose synthase from Deinococcus radiodurans reveals an open active-site topology
Resolution2.76 Å
Binding residue
(original residue number in PDB)		D24 N26 D28 K30 D32
Binding residue
(residue number reindexed from 1)		D19 N21 D23 K25 D27
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D101 R207 D209 E251 H318 D319
Catalytic site (residue number reindexed from 1) D96 R177 D179 E221 H288 D289
Enzyme Commision number 5.4.99.16: maltose alpha-D-glucosyltransferase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0016853 isomerase activity
GO:0046872 metal ion binding
GO:0047471 maltose alpha-D-glucosyltransferase activity
Biological Process
GO:0005975 carbohydrate metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5ykb, PDBe:5ykb, PDBj:5ykb
PDBsum5ykb
PubMed29095151
UniProtI3NX86

[Back to BioLiP]