Structure of PDB 6lgd Chain B Binding Site BS02

Receptor Information

>6lgd Chain B (length=570) Species: 7091 (Bombyx mori)

PPPTEVIQLDWWKNCVLYQIYPRSFKDSDGDGIGDLKGIISELKHFVDAG
VDAIWMSPIFESPMVDFGYDISNFYDIHYEYGTMEDFEELLDKAHELGLK
VLLDFVPNHASNESEYFIKSEAREPGYENFFIWADPLPNPENPGVRLPPS
NWVSQFGGSAWEWSEKRQQYYLHQFAIQQVDFDFRNPAVKQEMFNIMKFW
LDKGADGFRLDALPYLIEADPADHEGRYPDDPLSGLTQFESHQLGYTIPL
YTKDLIELYDVVYEWREFLDEYNKNHGGDTRVVFSEGYANVSMTMLYYGN
EDGAIGAHFPFNFDFITDLSSKSNARDFVYIILRWLTYMPYGGIPNWVFG
NHDNNRMPTRFRHDMVDGLNIINMLLPGVAVTYQGEEIGMRDGYVSWEDT
VDIEACNRGDPDTYHLYSRDPARTPYHWDNSTSAGFSTSTNTWLPVAEDY
QEINLAKQKETARSHFKNYQALTKLRKQATLSHGEYDIRALSDRTFYLVR
SLPTHDTYVLLFNVSERRDTVDLGRVPHLTLPATVYVSSIHSARLAGHEI
TSSQLSLEAGEALVLKAQPI

Ligand information

• Ligand ID: CA
• InChI: InChI=1S/Ca/q+2
• InChIKey: BHPQYMZQTOCNFJ-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Ca++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Ca+2]
• Formula: Ca
• Name: CALCIUM ION
• DrugBank: DB14577
• PDB chain: 6lgd Chain B Residue 702

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6lgd Structure-function analysis of silkworm sucrose hydrolase uncovers the mechanism of substrate specificity in GH13 subfamily 17exo-alpha-glucosidases.
• Resolution: 1.75 Å
• Binding residue (original residue number in PDB): N144 D217 Y251 L252 E254
• Binding residue (residue number reindexed from 1): N108 D181 Y215 L216 E218
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): D140 D247 E322 H388 D389
• Catalytic site (residue number reindexed from 1): D104 D211 E286 H352 D353
• Enzyme Commision number: 3.2.1.20: alpha-glucosidase.

Gene Ontology

Molecular Function

• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0005975 carbohydrate metabolic process

External links

• PDB: RCSB:6lgd, PDBe:6lgd, PDBj:6lgd
• PDBsum: 6lgd
• PubMed: 32381508
• UniProt: A0A077JI83