Structure of PDB 1e72 Chain M Binding Site BS02

Receptor Information

>1e72 Chain M (length=499) Species: 3728 (Sinapis alba)

EITCQENLPFTCGNTDALNSSSFSSDFIFGVASSAYQIEGTIGRGLNIWD
GFTHRYPNKSGPDHGNGDTTCDSFSYWQKDIDVLDELNATGYRFSIAWSR
IIPRGKRSRGVNEKGIDYYHGLISGLIKKGITPFVTLFHWDLPQTLQDEY
EGFLDPQIIDDFKDYADLCFEEFGDSVKYWLTINQLYSVPTRGYGSALDA
PGRCSPTVDPSCYAGNSSTEPYIVAHHQLLAHAKVVDLYRKNYTHQGGKI
GPTMITRWFLPYNDTDRHSIAATERMKEFFLGWFMGPLTNGTYPQIMIDT
VGERLPSFSPEESNLVKGSYDFLGLNYYFTQYAQPSPNPVNSTNHTAMMD
AGAKLTYINASGHYIGPLFEKDKADSTDNIYYYPKGIYSVMDYFKNKYYN
PLIYVTENGISTPGDENRNQSMLDYTRIDYLCSHLCFLNKVIKEKDVNVK
GYLAWALGDNYEFNKGFTVRFGLSYIDWNNVTDRDLKKSGQWYQSFISP

Ligand information

• Ligand ID: GOX
• InChI: InChI=1S/C6H12N2O5/c9-1-2-3(10)4(11)5(12)6(7-2)8-13/h2-5,9-13H,1H2,(H,7,8)/t2-,3-,4+,5-/m1/s1
• InChIKey: VBXHGXTYZGYTQG-SQOUGZDYSA-N
• SMILES:
  OpenEye OEToolkits 1.7.5: C(C1C(C(C(C(=NO)N1)O)O)O)O
  OpenEye OEToolkits 1.7.5: C([C@@H]1[C@H]([C@@H]([C@H](/C(=N/O)/N1)O)O)O)O
  CACTVS 3.385: OC[CH]1NC(=NO)[CH](O)[CH](O)[CH]1O
  CACTVS 3.385: OC[C@H]1NC(=N\O)/[C@H](O)[C@@H](O)[C@@H]1O
  ACDLabs 10.04: OC1C(O)C(O)C(=N\O)\NC1CO
• Formula: C6 H12 N2 O5
• Name: (2S,3S,4R,5R)-6-(HYDROXYAMINO)-2-(HYDROXYMETHYL)-2,3,4,5-TETRAHYDROPYRIDINE-3,4,5-TRIOL;
  D-GLUCONHYDROXIMO-1,5-LACTAM
• ChEMBL: CHEMBL1213470
• DrugBank: DB02376
• PDB chain: 1e72 Chain M Residue 999

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1e72 High resolution X-ray crystallography shows that ascorbate is a cofactor for myrosinase and substitutes for the function of the catalytic base.
• Resolution: 1.6 Å
• Binding residue (original residue number in PDB): Q39 H141 N186 Q187 Y330 E409 W457 E464 F465 F473
• Binding residue (residue number reindexed from 1): Q37 H139 N184 Q185 Y328 E407 W455 E462 F463 F471
• Annotation score: 1
• Binding affinity: MOAD: Ki=0.6mM
  PDBbind-CN: -logKd/Ki=3.22,Ki=0.6mM

Enzymatic activity

• Enzyme Commision number: 3.2.1.147: thioglucosidase.

Gene Ontology

Molecular Function

• GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
• GO:0008422 beta-glucosidase activity
• GO:0016798 hydrolase activity, acting on glycosyl bonds
• GO:0019137 thioglucosidase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0005975 carbohydrate metabolic process
• GO:0009651 response to salt stress
• GO:0019762 glucosinolate catabolic process

Cellular Component

• GO:0005773 vacuole

External links

• PDB: RCSB:1e72, PDBe:1e72, PDBj:1e72
• PDBsum: 1e72
• PubMed: 10978344
• UniProt: P29736|MYRA_SINAL Myrosinase MA1