5NDF
Small-molecule inhibition of ppGalNAc-Ts selectively reduces mucin-type O-glycosylation
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000139 | cellular_component | Golgi membrane |
| A | 0002639 | biological_process | positive regulation of immunoglobulin production |
| A | 0004653 | molecular_function | polypeptide N-acetylgalactosaminyltransferase activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005576 | cellular_component | extracellular region |
| A | 0005789 | cellular_component | endoplasmic reticulum membrane |
| A | 0005794 | cellular_component | Golgi apparatus |
| A | 0005795 | cellular_component | Golgi stack |
| A | 0006486 | biological_process | protein glycosylation |
| A | 0006493 | biological_process | protein O-linked glycosylation |
| A | 0016020 | cellular_component | membrane |
| A | 0016266 | biological_process | core O-glycan biosynthetic process |
| A | 0016740 | molecular_function | transferase activity |
| A | 0016757 | molecular_function | glycosyltransferase activity |
| A | 0018242 | biological_process | protein O-linked glycosylation via serine |
| A | 0018243 | biological_process | protein O-linked glycosylation via threonine |
| A | 0030145 | molecular_function | manganese ion binding |
| A | 0030246 | molecular_function | carbohydrate binding |
| A | 0032580 | cellular_component | Golgi cisterna membrane |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0048471 | cellular_component | perinuclear region of cytoplasm |
| A | 0051604 | biological_process | protein maturation |
| B | 0000139 | cellular_component | Golgi membrane |
| B | 0002639 | biological_process | positive regulation of immunoglobulin production |
| B | 0004653 | molecular_function | polypeptide N-acetylgalactosaminyltransferase activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005576 | cellular_component | extracellular region |
| B | 0005789 | cellular_component | endoplasmic reticulum membrane |
| B | 0005794 | cellular_component | Golgi apparatus |
| B | 0005795 | cellular_component | Golgi stack |
| B | 0006486 | biological_process | protein glycosylation |
| B | 0006493 | biological_process | protein O-linked glycosylation |
| B | 0016020 | cellular_component | membrane |
| B | 0016266 | biological_process | core O-glycan biosynthetic process |
| B | 0016740 | molecular_function | transferase activity |
| B | 0016757 | molecular_function | glycosyltransferase activity |
| B | 0018242 | biological_process | protein O-linked glycosylation via serine |
| B | 0018243 | biological_process | protein O-linked glycosylation via threonine |
| B | 0030145 | molecular_function | manganese ion binding |
| B | 0030246 | molecular_function | carbohydrate binding |
| B | 0032580 | cellular_component | Golgi cisterna membrane |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0048471 | cellular_component | perinuclear region of cytoplasm |
| B | 0051604 | biological_process | protein maturation |
| C | 0000139 | cellular_component | Golgi membrane |
| C | 0002639 | biological_process | positive regulation of immunoglobulin production |
| C | 0004653 | molecular_function | polypeptide N-acetylgalactosaminyltransferase activity |
| C | 0005515 | molecular_function | protein binding |
| C | 0005576 | cellular_component | extracellular region |
| C | 0005789 | cellular_component | endoplasmic reticulum membrane |
| C | 0005794 | cellular_component | Golgi apparatus |
| C | 0005795 | cellular_component | Golgi stack |
| C | 0006486 | biological_process | protein glycosylation |
| C | 0006493 | biological_process | protein O-linked glycosylation |
| C | 0016020 | cellular_component | membrane |
| C | 0016266 | biological_process | core O-glycan biosynthetic process |
| C | 0016740 | molecular_function | transferase activity |
| C | 0016757 | molecular_function | glycosyltransferase activity |
| C | 0018242 | biological_process | protein O-linked glycosylation via serine |
| C | 0018243 | biological_process | protein O-linked glycosylation via threonine |
| C | 0030145 | molecular_function | manganese ion binding |
| C | 0030246 | molecular_function | carbohydrate binding |
| C | 0032580 | cellular_component | Golgi cisterna membrane |
| C | 0046872 | molecular_function | metal ion binding |
| C | 0048471 | cellular_component | perinuclear region of cytoplasm |
| C | 0051604 | biological_process | protein maturation |
| D | 0000139 | cellular_component | Golgi membrane |
| D | 0002639 | biological_process | positive regulation of immunoglobulin production |
| D | 0004653 | molecular_function | polypeptide N-acetylgalactosaminyltransferase activity |
| D | 0005515 | molecular_function | protein binding |
| D | 0005576 | cellular_component | extracellular region |
| D | 0005789 | cellular_component | endoplasmic reticulum membrane |
| D | 0005794 | cellular_component | Golgi apparatus |
| D | 0005795 | cellular_component | Golgi stack |
| D | 0006486 | biological_process | protein glycosylation |
| D | 0006493 | biological_process | protein O-linked glycosylation |
| D | 0016020 | cellular_component | membrane |
| D | 0016266 | biological_process | core O-glycan biosynthetic process |
| D | 0016740 | molecular_function | transferase activity |
| D | 0016757 | molecular_function | glycosyltransferase activity |
| D | 0018242 | biological_process | protein O-linked glycosylation via serine |
| D | 0018243 | biological_process | protein O-linked glycosylation via threonine |
| D | 0030145 | molecular_function | manganese ion binding |
| D | 0030246 | molecular_function | carbohydrate binding |
| D | 0032580 | cellular_component | Golgi cisterna membrane |
| D | 0046872 | molecular_function | metal ion binding |
| D | 0048471 | cellular_component | perinuclear region of cytoplasm |
| D | 0051604 | biological_process | protein maturation |
| E | 0000139 | cellular_component | Golgi membrane |
| E | 0002639 | biological_process | positive regulation of immunoglobulin production |
| E | 0004653 | molecular_function | polypeptide N-acetylgalactosaminyltransferase activity |
| E | 0005515 | molecular_function | protein binding |
| E | 0005576 | cellular_component | extracellular region |
| E | 0005789 | cellular_component | endoplasmic reticulum membrane |
| E | 0005794 | cellular_component | Golgi apparatus |
| E | 0005795 | cellular_component | Golgi stack |
| E | 0006486 | biological_process | protein glycosylation |
| E | 0006493 | biological_process | protein O-linked glycosylation |
| E | 0016020 | cellular_component | membrane |
| E | 0016266 | biological_process | core O-glycan biosynthetic process |
| E | 0016740 | molecular_function | transferase activity |
| E | 0016757 | molecular_function | glycosyltransferase activity |
| E | 0018242 | biological_process | protein O-linked glycosylation via serine |
| E | 0018243 | biological_process | protein O-linked glycosylation via threonine |
| E | 0030145 | molecular_function | manganese ion binding |
| E | 0030246 | molecular_function | carbohydrate binding |
| E | 0032580 | cellular_component | Golgi cisterna membrane |
| E | 0046872 | molecular_function | metal ion binding |
| E | 0048471 | cellular_component | perinuclear region of cytoplasm |
| E | 0051604 | biological_process | protein maturation |
| F | 0000139 | cellular_component | Golgi membrane |
| F | 0002639 | biological_process | positive regulation of immunoglobulin production |
| F | 0004653 | molecular_function | polypeptide N-acetylgalactosaminyltransferase activity |
| F | 0005515 | molecular_function | protein binding |
| F | 0005576 | cellular_component | extracellular region |
| F | 0005789 | cellular_component | endoplasmic reticulum membrane |
| F | 0005794 | cellular_component | Golgi apparatus |
| F | 0005795 | cellular_component | Golgi stack |
| F | 0006486 | biological_process | protein glycosylation |
| F | 0006493 | biological_process | protein O-linked glycosylation |
| F | 0016020 | cellular_component | membrane |
| F | 0016266 | biological_process | core O-glycan biosynthetic process |
| F | 0016740 | molecular_function | transferase activity |
| F | 0016757 | molecular_function | glycosyltransferase activity |
| F | 0018242 | biological_process | protein O-linked glycosylation via serine |
| F | 0018243 | biological_process | protein O-linked glycosylation via threonine |
| F | 0030145 | molecular_function | manganese ion binding |
| F | 0030246 | molecular_function | carbohydrate binding |
| F | 0032580 | cellular_component | Golgi cisterna membrane |
| F | 0046872 | molecular_function | metal ion binding |
| F | 0048471 | cellular_component | perinuclear region of cytoplasm |
| F | 0051604 | biological_process | protein maturation |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | binding site for residue MN A 601 |
| Chain | Residue |
| A | ASP224 |
| A | HIS226 |
| A | HIS359 |
| A | UDP602 |
| A | HOH768 |
| site_id | AC2 |
| Number of Residues | 22 |
| Details | binding site for residue UDP A 602 |
| Chain | Residue |
| A | ARG201 |
| A | GLY203 |
| A | LEU204 |
| A | ASP224 |
| A | SER225 |
| A | HIS226 |
| A | VAL330 |
| A | TRP331 |
| A | HIS359 |
| A | ARG362 |
| A | TYR367 |
| A | MN601 |
| A | EDO605 |
| A | HOH747 |
| A | HOH756 |
| A | HOH768 |
| A | HOH796 |
| A | HOH813 |
| A | THR143 |
| A | PHE144 |
| A | HIS145 |
| A | ASP176 |
| site_id | AC3 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 603 |
| Chain | Residue |
| A | ILE252 |
| A | ILE253 |
| A | SER267 |
| A | ALA268 |
| A | LEU270 |
| A | TRP282 |
| A | LU2608 |
| site_id | AC4 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 604 |
| Chain | Residue |
| A | LEU204 |
| A | ALA307 |
| A | GLY308 |
| A | GLY309 |
| A | TRP331 |
| A | GLY332 |
| A | GLU334 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 605 |
| Chain | Residue |
| A | ALA307 |
| A | GLY309 |
| A | HIS359 |
| A | PHE361 |
| A | UDP602 |
| site_id | AC6 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 606 |
| Chain | Residue |
| A | PRO557 |
| A | GLN562 |
| D | TYR99 |
| site_id | AC7 |
| Number of Residues | 2 |
| Details | binding site for residue EDO A 607 |
| Chain | Residue |
| A | GLU391 |
| A | HIS442 |
| site_id | AC8 |
| Number of Residues | 8 |
| Details | binding site for residue LU2 A 608 |
| Chain | Residue |
| A | ILE253 |
| A | LEU270 |
| A | PHE361 |
| A | LYS363 |
| A | EDO603 |
| A | HOH702 |
| A | HOH705 |
| B | PHE463 |
| site_id | AC9 |
| Number of Residues | 4 |
| Details | binding site for residue MN B 601 |
| Chain | Residue |
| B | ASP224 |
| B | HIS226 |
| B | HIS359 |
| B | UDP602 |
| site_id | AD1 |
| Number of Residues | 17 |
| Details | binding site for residue UDP B 602 |
| Chain | Residue |
| B | THR143 |
| B | PHE144 |
| B | HIS145 |
| B | ASP176 |
| B | ARG201 |
| B | GLY203 |
| B | LEU204 |
| B | ASP224 |
| B | SER225 |
| B | HIS226 |
| B | VAL330 |
| B | TRP331 |
| B | HIS359 |
| B | ARG362 |
| B | TYR367 |
| B | MN601 |
| B | EDO603 |
| site_id | AD2 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 603 |
| Chain | Residue |
| B | ALA307 |
| B | TRP331 |
| B | GLU334 |
| B | UDP602 |
| site_id | AD3 |
| Number of Residues | 7 |
| Details | binding site for residue LU2 B 604 |
| Chain | Residue |
| A | PHE463 |
| B | ILE253 |
| B | ALA266 |
| B | LEU270 |
| B | TRP282 |
| B | PHE361 |
| B | LYS363 |
| site_id | AD4 |
| Number of Residues | 5 |
| Details | binding site for residue MN C 601 |
| Chain | Residue |
| C | ASP224 |
| C | HIS226 |
| C | HIS359 |
| C | UDP602 |
| C | HOH744 |
| site_id | AD5 |
| Number of Residues | 17 |
| Details | binding site for residue UDP C 602 |
| Chain | Residue |
| C | ASP176 |
| C | ARG201 |
| C | GLY203 |
| C | LEU204 |
| C | ASP224 |
| C | SER225 |
| C | HIS226 |
| C | VAL330 |
| C | TRP331 |
| C | HIS359 |
| C | ARG362 |
| C | TYR367 |
| C | MN601 |
| C | HOH744 |
| C | THR143 |
| C | PHE144 |
| C | HIS145 |
| site_id | AD6 |
| Number of Residues | 3 |
| Details | binding site for residue EDO C 603 |
| Chain | Residue |
| C | ASN198 |
| C | ASP199 |
| C | GLU202 |
| site_id | AD7 |
| Number of Residues | 4 |
| Details | binding site for residue MN D 601 |
| Chain | Residue |
| D | ASP224 |
| D | HIS226 |
| D | HIS359 |
| D | UDP602 |
| site_id | AD8 |
| Number of Residues | 16 |
| Details | binding site for residue UDP D 602 |
| Chain | Residue |
| D | THR143 |
| D | PHE144 |
| D | HIS145 |
| D | ASP176 |
| D | ARG201 |
| D | LEU204 |
| D | ASP224 |
| D | SER225 |
| D | HIS226 |
| D | TRP331 |
| D | HIS359 |
| D | ARG362 |
| D | TYR367 |
| D | MN601 |
| D | HOH745 |
| D | HOH776 |
| site_id | AD9 |
| Number of Residues | 6 |
| Details | binding site for residue EDO D 603 |
| Chain | Residue |
| D | ASN198 |
| D | ASP199 |
| D | GLU202 |
| D | ARG210 |
| D | HOH725 |
| D | HOH782 |
| site_id | AE1 |
| Number of Residues | 7 |
| Details | binding site for residue LU2 D 604 |
| Chain | Residue |
| D | ILE253 |
| D | LEU270 |
| D | PHE361 |
| D | LYS363 |
| D | HOH713 |
| D | HOH769 |
| F | PHE463 |
| site_id | AE2 |
| Number of Residues | 5 |
| Details | binding site for residue MN E 601 |
| Chain | Residue |
| E | ASP224 |
| E | HIS226 |
| E | HIS359 |
| E | UDP602 |
| E | HOH728 |
| site_id | AE3 |
| Number of Residues | 20 |
| Details | binding site for residue UDP E 602 |
| Chain | Residue |
| E | THR143 |
| E | PHE144 |
| E | HIS145 |
| E | ASP176 |
| E | ARG201 |
| E | GLY203 |
| E | LEU204 |
| E | ASP224 |
| E | SER225 |
| E | HIS226 |
| E | VAL330 |
| E | TRP331 |
| E | HIS359 |
| E | ARG362 |
| E | TYR367 |
| E | MN601 |
| E | EDO603 |
| E | HOH721 |
| E | HOH728 |
| E | HOH756 |
| site_id | AE4 |
| Number of Residues | 6 |
| Details | binding site for residue EDO E 603 |
| Chain | Residue |
| E | GLY308 |
| E | GLY309 |
| E | TRP331 |
| E | GLY332 |
| E | GLU334 |
| E | UDP602 |
| site_id | AE5 |
| Number of Residues | 4 |
| Details | binding site for residue MN F 601 |
| Chain | Residue |
| F | ASP224 |
| F | HIS226 |
| F | HIS359 |
| F | UDP602 |
| site_id | AE6 |
| Number of Residues | 15 |
| Details | binding site for residue UDP F 602 |
| Chain | Residue |
| F | THR143 |
| F | PHE144 |
| F | HIS145 |
| F | ASP176 |
| F | ARG201 |
| F | GLY203 |
| F | LEU204 |
| F | ASP224 |
| F | SER225 |
| F | HIS226 |
| F | TRP331 |
| F | HIS359 |
| F | ARG362 |
| F | TYR367 |
| F | MN601 |
| site_id | AE7 |
| Number of Residues | 5 |
| Details | binding site for residue EDO F 603 |
| Chain | Residue |
| F | LEU484 |
| F | LYS488 |
| F | TRP522 |
| F | GLU523 |
| F | GLN524 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 30 |
| Details | TOPO_DOM: Cytoplasmic => ECO:0000255 |
| Chain | Residue | Details |
| A | MET1-ARG6 | |
| B | MET1-ARG6 | |
| C | MET1-ARG6 | |
| D | MET1-ARG6 | |
| E | MET1-ARG6 | |
| F | MET1-ARG6 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 102 |
| Details | TRANSMEM: Helical; Signal-anchor for type II membrane protein => ECO:0000255 |
| Chain | Residue | Details |
| A | MET7-TYR24 | |
| B | MET7-TYR24 | |
| C | MET7-TYR24 | |
| D | MET7-TYR24 | |
| E | MET7-TYR24 | |
| F | MET7-TYR24 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 3276 |
| Details | TOPO_DOM: Lumenal => ECO:0000255 |
| Chain | Residue | Details |
| A | SER25-GLN571 | |
| B | SER25-GLN571 | |
| C | SER25-GLN571 | |
| D | SER25-GLN571 | |
| E | SER25-GLN571 | |
| F | SER25-GLN571 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 42 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:16434399, ECO:0000269|PubMed:24954443, ECO:0000269|PubMed:25939779, ECO:0007744|PDB:2FFU, ECO:0007744|PDB:2FFV, ECO:0007744|PDB:4D0T, ECO:0007744|PDB:4D11, ECO:0007744|PDB:5AJP, ECO:0007744|PDB:5FV9 |
| Chain | Residue | Details |
| A | THR143 | |
| B | ARG201 | |
| B | SER225 | |
| B | TRP331 | |
| B | ARG362 | |
| B | HIS365 | |
| C | THR143 | |
| C | ASP176 | |
| C | ARG201 | |
| C | SER225 | |
| C | TRP331 | |
| A | ASP176 | |
| C | ARG362 | |
| C | HIS365 | |
| D | THR143 | |
| D | ASP176 | |
| D | ARG201 | |
| D | SER225 | |
| D | TRP331 | |
| D | ARG362 | |
| D | HIS365 | |
| E | THR143 | |
| A | ARG201 | |
| E | ASP176 | |
| E | ARG201 | |
| E | SER225 | |
| E | TRP331 | |
| E | ARG362 | |
| E | HIS365 | |
| F | THR143 | |
| F | ASP176 | |
| F | ARG201 | |
| F | SER225 | |
| A | SER225 | |
| F | TRP331 | |
| F | ARG362 | |
| F | HIS365 | |
| A | TRP331 | |
| A | ARG362 | |
| A | HIS365 | |
| B | THR143 | |
| B | ASP176 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 18 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:16434399, ECO:0000269|PubMed:24954443, ECO:0000269|PubMed:25939779, ECO:0007744|PDB:2FFU, ECO:0007744|PDB:2FFV, ECO:0007744|PDB:4D0T, ECO:0007744|PDB:4D0Z, ECO:0007744|PDB:4D11, ECO:0007744|PDB:5AJP, ECO:0007744|PDB:5FV9 |
| Chain | Residue | Details |
| A | ASP224 | |
| D | ASP224 | |
| D | HIS226 | |
| D | HIS359 | |
| E | ASP224 | |
| E | HIS226 | |
| E | HIS359 | |
| F | ASP224 | |
| F | HIS226 | |
| F | HIS359 | |
| A | HIS226 | |
| A | HIS359 | |
| B | ASP224 | |
| B | HIS226 | |
| B | HIS359 | |
| C | ASP224 | |
| C | HIS226 | |
| C | HIS359 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:16434399, ECO:0000269|PubMed:24954443, ECO:0000269|PubMed:25939779, ECO:0007744|PDB:2FFU, ECO:0007744|PDB:2FFV, ECO:0007744|PDB:4D0T, ECO:0007744|PDB:4D0Z, ECO:0007744|PDB:4D11, ECO:0007744|PDB:5AJN, ECO:0007744|PDB:5AJO, ECO:0007744|PDB:5AJP, ECO:0007744|PDB:5FV9, ECO:0007744|PDB:5NDF, ECO:0007744|PDB:6EGS |
| Chain | Residue | Details |
| A | TYR367 | |
| B | TYR367 | |
| C | TYR367 | |
| D | TYR367 | |
| E | TYR367 | |
| F | TYR367 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 6 |
| Details | SITE: Not glycosylated |
| Chain | Residue | Details |
| A | ASP516 | |
| B | ASP516 | |
| C | ASP516 | |
| D | ASP516 | |
| E | ASP516 | |
| F | ASP516 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 6 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER536 | |
| B | SER536 | |
| C | SER536 | |
| D | SER536 | |
| E | SER536 | |
| F | SER536 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 6 |
| Details | CARBOHYD: O-linked (Xyl...) (chondroitin sulfate) serine => ECO:0000269|PubMed:37453717 |
| Chain | Residue | Details |
| A | SER29 | |
| B | SER29 | |
| C | SER29 | |
| D | SER29 | |
| E | SER29 | |
| F | SER29 |
