Structure of PDB 5ykb Chain A Binding Site BS02

Receptor Information

>5ykb Chain A (length=529) Species: 243230 (Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)

PEWYKSAVFYELSVRTFQDGNGDGKGDFPGLTSRLDYLKNLGVDCLWLLP
WFPSPLRDDGYDVADYRGIHPDLGTLDDFKVFLREAHARGLWVIGDLVTN
HTSSDHPWFQAARRGPTLPDGSPNEYHDYYVWSDNWTLDEQAGKYYWHRF
FASQPDLNYDNPKVVEELHGAARFWLDLGLDGFRVDAVPYLIEREGTSCE
NLPETHEILKGFRAMVDREYPGRLLLAEAFQWPEEVVEYFGTEAEPEFHM
CFNFPVMPRLYMSLKREDTSSIREIMGRLPKIPSFGQWCIFLRNHDELTL
EMVTDDERAFMYAAYAPDARMKINVGIRRRLAPLLDNDRRRIELLNTVLL
ALPGSPVLYYGDEIGMGDDLGLPDRNGVRTPMQWNAGTSGGFSTAQPSDC
FFPPIQDPVYGFGRVNVQSQLQDPSSLLKWTARQLELRRAHPAFAHGDLT
FIETGNPAILAFTRQYDGETLLIVSNFAGNAQAGLLDLAPFVGRAPVTLS
GASPLPVVTGNGQYPVVMGKYDYYWLRLN

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 5ykb Chain A Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ykb The N253F mutant structure of trehalose synthase from Deinococcus radiodurans reveals an open active-site topology
• Resolution: 2.76 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 score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D101 R207 D209 E251 H318 D319
• Catalytic site (residue number reindexed from 1): D96 R184 D186 E228 H295 D296
• 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

External links

• PDB: RCSB:5ykb, PDBe:5ykb, PDBj:5ykb
• PDBsum: 5ykb
• PubMed: 29095151
• UniProt: I3NX86