Structure of PDB 4gpn Chain A Binding Site BS01

Receptor Information

>4gpn Chain A (length=478) Species: 210007 (Streptococcus mutans UA159)

AMSKLPENFLWGGAVAAHQLEGGWQEGGKGISVADVMTAGRHGVAREITA
GVLEGKYYPNHEAIDFYHHYKEDVKLFAEMGFKCFRTSIAWTRIFPKGDE
AEPNEAGLQFYDDLFDECLKYGIEPVVTLSHFELPYHLVTEYGGFTNRKV
IDFFVHFAEVCFRRYKDKVKYWMTFNEINNQANYQEDFAPFTNSGIVYKE
GDDREAIMYQAAHYELVASARAVKIGHAINPNLNIGCMVAMCPIYPATCN
PKDILMAQKAMQKRYYFADVHVHGFYPEHIFKYWERKAIKVDFTERDKKD
LFEGTVDYIGFSYYMSFVIDAHRENNPYYDYLETEDLVKNPYVKASDWDW
QIDPQGLRYALNWFTDMYHLPLFIVQNGFGAIDQVEADGMVHDDYRIDYL
GAHIKEMIKAVDEDGVELMGYTPWGCIDLVSAGTGEMRKRYGFIYVDKDD
EGKGTLKRSPKLSFNWYKEVIASNGDDI

Ligand information

• Ligand ID: BG6
• InChI: InChI=1S/C6H13O9P/c7-3-2(1-14-16(11,12)13)15-6(10)5(9)4(3)8/h2-10H,1H2,(H2,11,12,13)/t2-,3-,4+,5-,6-/m1/s1
• InChIKey: NBSCHQHZLSJFNQ-VFUOTHLCSA-N
• SMILES:
  CACTVS 3.341: O[CH]1O[CH](CO[P](O)(O)=O)[CH](O)[CH](O)[CH]1O
  OpenEye OEToolkits 1.5.0: C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O)O)O)O)OP(=O)(O)O
  CACTVS 3.341: O[C@@H]1O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H](O)[C@H]1O
  OpenEye OEToolkits 1.5.0: C(C1C(C(C(C(O1)O)O)O)O)OP(=O)(O)O
  ACDLabs 10.04: O=P(O)(O)OCC1OC(O)C(O)C(O)C1O
• Formula: C6 H13 O9 P
• Name: 6-O-phosphono-beta-D-glucopyranose;
  BETA-D-GLUCOSE-6-PHOSPHATE;
  6-O-phosphono-beta-D-glucose;
  6-O-phosphono-D-glucose;
  6-O-phosphono-glucose
• ChEMBL: CHEMBL257975
• DrugBank: DB04122
• ZINC: ZINC000003875374
• PDB chain: 4gpn Chain C Residue 2

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4gpn GH1-family 6-P-beta-glucosidases from human microbiome lactic acid bacteria.
• Resolution: 2.291 Å
• Binding residue (original residue number in PDB): Q18 H130 E176 Y313 W349 Q375 W423 S430 A431 G432 K438 Y440
• Binding residue (residue number reindexed from 1): Q19 H131 E177 Y314 W350 Q376 W424 S431 A432 G433 K439 Y441
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): R85 H130 E176 N179 S311 Y313 Q375
• Catalytic site (residue number reindexed from 1): R86 H131 E177 N180 S312 Y314 Q376
• Enzyme Commision number: 3.2.1.86: 6-phospho-beta-glucosidase.

Gene Ontology

Molecular Function

• GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
• GO:0008422 beta-glucosidase activity
• GO:0008706 6-phospho-beta-glucosidase activity
• GO:0016798 hydrolase activity, acting on glycosyl bonds

Biological Process

• GO:0005975 carbohydrate metabolic process
• GO:0016052 carbohydrate catabolic process

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:4gpn, PDBe:4gpn, PDBj:4gpn
• PDBsum: 4gpn
• PubMed: 23519420
• UniProt: Q8DT00