Structure of PDB 5kzw Chain A Binding Site BS01

Receptor Information

>5kzw Chain A (length=850) Species: 9606 (Homo sapiens)

PTQCDVPPNSRFDCAPDKAITQEQCEARGCCYIPAKQMGQPWCFFPPSYP
SYKLENLSSSEMGYTATLTRTTPTFFPKDILTLRLDVMMETENRLHFTIK
DPANRRYEVPLETPSPLYSVEFSEEPFGVIVHRQLDGRVLLNTTVAPLFF
ADQFLQLSTSLPSQYITGLAEHLSPLMLSTSWTRITLWNRDLAPTPGANL
YGSHPFYLALEDGGSAHGVFLLNSNAMDVVLQPSPALSWRSTGGILDVYI
FLGPEPKSVVQQYLDVVGYPFMPPYWGLGFHLCRWGYSSTAITRQVVENM
TRAHFPLDVQWNDLDYMDSRRDFTFNKDGFRDFPAMVQELHQGGRRYMMI
VDPAISSSGPAGSYRPYDEGLRRGVFITNETGQPLIGKVWPGSTAFPDFT
NPTALAWWEDMVAEFHDQVPFDGMWIDMNEPSNFIRGSEDGCPNNELENP
PYVPGVVGGTLQAATICASSHQFLSTHYNLHNLYGLTEAIASHRALVKAR
GTRPFVISRSTFAGHGRYAGHWTGDVWSSWEQLASSVPEILQFNLLGVPL
VGADVCGFLGNTSEELCVRWTQLGAFYPFMRNHNSLLSLPQEPYSFSEPA
QQAMRKALTLRYALLPHLYTLFHQAHVAGETVARPLFLEFPKDSSTWTVD
HQLLWGEALLITPVLQAGKAEVTGYFPLGTWYDLQTVPIEPREPAIHSEG
QWVTLPAPLDTINVHLRAGYIIPLQGPGLTTTESRQQPMALAVALTKGGE
ARGELFWDDGESLEVLERGAYTQVIFLARNNTIVNELVRVTSEGAGLQLQ
KVTVLGVATAPQQVLSNGVPVSNFTYSPDTKVLDICVSLLMGEQFLVSWC

Ligand information

• Ligand ID: GLC
• InChI: InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6+/m1/s1
• InChIKey: WQZGKKKJIJFFOK-DVKNGEFBSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C(C1C(C(C(C(O1)O)O)O)O)O
  OpenEye OEToolkits 1.5.0: C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)O)O
  CACTVS 3.341: OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
  CACTVS 3.341: OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@H]1O
  ACDLabs 10.04: OC1C(O)C(OC(O)C1O)CO
• Formula: C6 H12 O6
• Name: alpha-D-glucopyranose;
  alpha-D-glucose;
  D-glucose;
  glucose
• ChEMBL: CHEMBL423707
• ZINC: ZINC000003861213
• PDB chain: 5kzw Chain A Residue 1014

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5kzw The structure of human GAA: structural basis of Pompe disease
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): W376 D404 L405 D518 R600 D616 F649 H674
• Binding residue (residue number reindexed from 1): W285 D313 L314 D427 R509 D525 F558 H583
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 3.2.1.20: alpha-glucosidase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
• GO:0004558 alpha-1,4-glucosidase activity
• GO:0016798 hydrolase activity, acting on glycosyl bonds
• GO:0030246 carbohydrate binding
• GO:0090599 alpha-glucosidase activity

Biological Process

• GO:0000023 maltose metabolic process
• GO:0002026 regulation of the force of heart contraction
• GO:0002086 diaphragm contraction
• GO:0003007 heart morphogenesis
• GO:0005975 carbohydrate metabolic process
• GO:0005977 glycogen metabolic process
• GO:0005980 glycogen catabolic process
• GO:0005985 sucrose metabolic process
• GO:0006006 glucose metabolic process
• GO:0006941 striated muscle contraction
• GO:0007040 lysosome organization
• GO:0007626 locomotory behavior
• GO:0009888 tissue development
• GO:0035904 aorta development
• GO:0043181 vacuolar sequestering
• GO:0046716 muscle cell cellular homeostasis
• GO:0050884 neuromuscular process controlling posture
• GO:0050885 neuromuscular process controlling balance
• GO:0060048 cardiac muscle contraction
• GO:0061723 glycophagy

Cellular Component

• GO:0005764 lysosome
• GO:0005765 lysosomal membrane
• GO:0005886 plasma membrane
• GO:0016020 membrane
• GO:0035577 azurophil granule membrane
• GO:0043202 lysosomal lumen
• GO:0043231 intracellular membrane-bounded organelle
• GO:0070062 extracellular exosome
• GO:0070821 tertiary granule membrane
• GO:0101003 ficolin-1-rich granule membrane
• GO:0120282 autolysosome lumen

External links

• PDB: RCSB:5kzw, PDBe:5kzw, PDBj:5kzw
• PDBsum: 5kzw
• UniProt: P10253|LYAG_HUMAN Lysosomal alpha-glucosidase (Gene Name=GAA)